[ccp4bb] Postdoctoral position in Brisbane, Australia
Applications are invited for a post-doctoral position in the group of Bostjan Kobe at the School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, Australia. We are searching for a motivated candidate to study the structure, function and drug targeting of TIR domain-containing proteins in humans. Experience with cryo-electron microscopy and drug design are particularly desirable. University of Queensland is one of Australia's top universities. SCMB combines the disciplines of chemistry, biochemistry & molecular biology, microbiology and parasitology into a single academic unit. SCMB is situated in the beautiful St. Lucia campus on the Brisbane River. Facilities are available on campus for all relevant techniques (including JEOL Cryo ARM 300 and 200 and Thermo Fisher Glacios electron microscopes, instruments for various biophysical techniques (including ITC, SPR, MALS, mass photometry), NMR, and automated crystallization), and there is regular access to the Australian Synchrotron. Brisbane is one of Australia's most liveable cities and has a fantastic subtropical climate. It is only a short drive from Australia's best beaches and provides opportunities for all sorts of outdoors and cultural activities. The salary will be according to qualifications and experience. The position will be initially for 1 year but may be extended, depending on available funding. The starting date is flexible. The application deadline is 13 August 2024. Please see the links below for details of the positions and application procedures. Web link: https://uq.wd3.myworkdayjobs.com/uqcareers/job/St-Lucia-Campus/Postdoctoral-Research-Fellow---Structural-Biology-and-Drug-Design_R-40802 Please contact Bostjan Kobe (email b.k...@uq.edu.au<mailto:b.k...@uq.edu.au>, telephone: +617-3365-2132,) for further information. -- Bostjan Kobe FAA NHMRC Investigator Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Australian Infectious Diseases Research Centre Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Future Diffraction Methods
Hi guys I would be a bit more optimistic about this idea… If people attend the meeting with the objective of building some bridges they will try. I have been to meetings on a biological topic where I may have been the only structural biologist but it was clear why I was there and I did not feel isolated, despite not being able to participate in every technical discussion on methods I am not familiar with. Bostjan -- Bostjan Kobe FAA Australian Laureate Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Australian Infectious Diseases Research Centre Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. From: CCP4 bulletin board on behalf of Nukri Sanishvili Reply to: Nukri Sanishvili Date: Monday, 30 January 2023 at 11:40 am To: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] Future Diffraction Methods Hi Pavel, Your description of the current status is exactly correct. And that's exactly what I am proposing to change or, more accurately, try to change. By seeking out and bringing together people who do complementary and collaborative work, so they can set an example for others. This, of course, isn't meant in place of more narrowly defined topical meetings and conferences but to be in addition to those. James asked the community if we had new ideas and this is a new-ish approach I was suggesting. Don't get me wrong - I myself will happily continue my efforts in more narrowly defined meetings. Best wishes, Nukri On Sun, Jan 29, 2023 at 6:44 PM Pavel Afonine mailto:pafon...@gmail.com>> wrote: Nukri, IMO, the idea of cross-discipline meetings is great conceptually, at least for reasons you pointed out, but utopical in practice. When we attend our field-specific meetings we meet colleagues we know, we talk to collaborators from the past or find new ones, we have things in common that we can talk about to forge something new, we meet authors of papers we were excited to read, and so on, and so on. I once attended a meeting of some chemistry society, well, which is not too far from what we are doing, really, as interpreting atomic models is essentially putting your chemistry knowledge into production. And, at that meeting I felt like I'm alone in a dark forest. Now, I imagine, if you bring two (or more) groups of people to your meeting from two different domains, well, I guess you will end up having two bubbles of people clustered by their field of interest. Same disclaimer goes here as yours -- no offence to any one, just thinking out loud... All the best! Pavel On Sun, Jan 29, 2023 at 6:09 AM Nukri Sanishvili mailto:sannu...@gmail.com>> wrote: Hi James, This meeting has indeed been one of the best ones by its format, content, and atmosphere. Many thanks to all the organizers and attendees of the past. Nevertheless, it is not surprising that it was cancelled, given the trends in structural biology research. Straightforward evolutionary pressure to adapt or else... Throughout my career I was always amazed (dare I say, annoyed?) how scientists from different fields, or even the same field but different methods, speak different languages. How little they understand each other, become entrenched in their own methods and how much of the collaboration/cooperation opportunities are wasted. IMO, having a conference on "Complementary Methods in Structural Biology" with the emphasis on complementarity and not on individual methods, would be a great benefit in the long run. Hopefully it would give good examples to young researchers to help them develop a collaborative mindset. If I offended anyone, it was not intentional, I promise, and apologize in advance. Best wishes to all and best of luck to all who continue the effort for the benefit of the whole community. Nukri On Fri, Dec 16, 2022 at 4:11 PM James Holton mailto:jmhol...@lbl.gov>> wrote: I want to thank everyone who attended the 2022 Gordon Research Conference and Gordon Research Seminar on Diffraction Methods in Structural Biology, as well as all those who contributed to these great gatherings in the past. It was an outstanding meeting if I do say so myself. Not just because it had been so long without in-person interaction, not just because we had zero covid cases (which I see as no small feat of Mind over Virus), but because of this amazing community. It is ra
Re: [ccp4bb] A challenging MR problem
Superimposing that molecule on all the others? Bostjan -- Bostjan Kobe FAA Australian Laureate Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Australian Infectious Diseases Research Centre Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. From: CCP4 bulletin board on behalf of Medhanjali DasGupta Reply to: Medhanjali DasGupta Date: Thursday, 10 November 2022 at 9:05 am To: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] A challenging MR problem The data resolution is 2A. I have 16 chains in my model out of which only one of the chains has the "missing" domain modeled. Is there a way to do MR to predict where the missing domains will go in the rest of the chains, based on my solved structure? Thanks for all the helpful suggestions!! M On Wed, Nov 9, 2022 at 3:11 PM Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote: Well you could just try the buccaneer pipeline. It would use the phases from your solved domain and try to fit the missing sequence. What are your twin fractions? And what is the resolution? Eleanor On Wed, 9 Nov 2022 at 21:06, Tim Gruene mailto:tim.gru...@univie.ac.at>> wrote: Dear Medhanjali DasGupta, unless the resolution is really poor, the quickest try would be shelxe, starting from what you already have. It might work at, say, 2.8A resolution or better... Best, Tim On Wed, 9 Nov 2022 14:34:28 -0600 Medhanjali DasGupta mailto:medhanjalidasgu...@gmail.com>> wrote: > Hello! > My protein structure has a missing domain and I am trying to figure > out the best way to model this missing domain using the solved > (modeled) fixed core domain? My data is also imperfectly twinned, > with 4 twin fractions according to refmac5. > > Any help/ idea is appreciated! > > > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- Thanks, Medhanjali Dasgupta Postdoctoral Research Scientist Lawrence Berkeley National Laboratory [Image removed by sender.] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PhD scholarship at the University of Queensland Brisbane Australia
Hi everyone We have a fully funded PhD scholarship at the University of Queensland in Brisbane Australia, to work on the structural biology of plant immune receptors. For more details, please see: https://graduate-school.uq.edu.au/project/structural-basis-plant-immune-receptor-signaling and contact Bostjan Kobe at b.k...@uq.edu.au. Please circulate this to potential candidates. The scholarship is open to international students. Best wishes Bostjan -- Bostjan Kobe FAA Australian Research Council Laureate Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand
Hi Fred Ligplot diagram is part of PDBsum output - maybe that will work for you. Bostjan -- Bostjan Kobe FAA Australian Research Council Laureate Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. On 6/4/21, 11:48 pm, "CCP4 bulletin board on behalf of Fred Vellieux" wrote: Hi folks, I'm trying to run Ligplot on a PDB file that contains a residue with type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 years now (which means that I had to reinstall, with an expired license, and get familiar with it again). I get the following error message (rather cryptic): Calling HBADD ... Running HBADD Het Group Dictionary: /components.cif Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb Command: /LigPlus/lib/exe_linux/hbadd /tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir /tmp/lig7141158588178475829/ java.io.IOException: Cannot run program "/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory Other event: state Would anyone know what to make out of this message ? Otherwise is there another piece of software (called "app" nowadays) that could provide me with similar drawings ? At some stage I ran PRODRG, introduced the cif file in the file components.cif used by LigPlot (LigPlus). I also replaced the coordinate files by those returned by the PRODRG run. Always with the same cryptic error message provided by the software (oops, app). Thanks, Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] crystallizing fusion proteins
Hi Herman I agree with all discussed already. First, is your protein of interest actually folded or just solubilized by the large fusion partner? If it is folded, worth considering crystallization of the fusion protein, as a “desperate measure” approach. The key issue will be making the linkage between the proteins reasonably rigid, to increase chances of crystallization. In GPCRs, T4L is usually inserted into a loop, which obviously will constrain it more than just one linkage at the terminus. There is quite a bit of literature on the topic already, and some nice tools like the MBP with increased crystallization propensity, as already pointed out. Let me know if I can help finding any key papers. But at the end of the day, my feeling is people try this a lot, as setting up some crystallization plates is easier than troubleshooting cleavage, purification and making and purifying new constructs. Despite this, other than specific cases like GPCRs, there are not that many successful examples really. So my feeling is this approach doesn’t work that often without a lot of trial and optimization. Best wishes Bostjan -- Bostjan Kobe FAA Australian Research Council Laureate Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. From: CCP4 bulletin board on behalf of Tao-Hsin Chang Reply to: Tao-Hsin Chang Date: Tuesday, 16 March 2021 at 6:55 am To: "CCP4BB@JISCMAIL.AC.UK" Subject: Re: [ccp4bb] crystallizing fusion proteins Hi Herman, We learned a few tricks of using MBP fusion for solving an interesting fold of a receptor extracellular domain from our recent publication (https://pubmed.ncbi.nlm.nih.gov/32541044/). (1) the length of a linker between MBP and protein of interest is critical. Use a computational modeling approach to figure out a reasonable linker, if possible. (2) take advantage of engineered MBP e.g., surface entropy reduction mutations and ion-mediated dimerization mutations (a good review https://pubmed.ncbi.nlm.nih.gov/26682969/; https://pubmed.ncbi.nlm.nih.gov/26850170/) that do help. (3) use either E. coli Shuffle cells or mammalian cells to deal with the disulfide bonds and characterize the protein folding e.g. CD or SEC (not ideal, but simple). Hope this helps. Best wishes, Tao-Hsin Tao-Hsin Chang, DPhil Research Specialist Howard Hughes Medical Institute On Mar 15, 2021, at 5:07 AM, Schreuder, Herman /DE mailto:herman.schreu...@sanofi.com>> wrote: Dear Bulletin Board, Sorry for the slightly off-topic question, but we are struggling with a receptor domain that expresses well as a fusion protein, but gets lost the moment it is cleaved from the fusion partner. It could be that the receptor domain is not or misfolded, but it could also be a solubility problem. I have seen some crystal structures of fusion proteins with MBP and for membrane proteins, T4-lysozyme fusions are often crystallized. What is your experience? Would it be worth trying to express and crystallize a fusion protein, or would it be better to look for other constructs, e.g. to include more receptor domains? Thank you very much for your advice! Herman To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Post-doctoral position at the University of Queensland, Brisbane, Australia
Applications are invited for a post-doctoral position in the group of Bostjan Kobe at the School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, Australia. We are searching for a motivated candidate, ideally with experience with cryo-electron microscopy, and/or other structural biology and protein biochemistry techniques, to study the structural basis of function of proteins involved in innate immunity pathways in plants. For some of our recent publications on related topics, please see https://www.ncbi.nlm.nih.gov/pubmed/28159890 , https://www.ncbi.nlm.nih.gov/pubmed/28759049 and https://www.ncbi.nlm.nih.gov/pubmed/24744375 . University of Queensland is one of Australia's top universities. SCMB combines the disciplines of chemistry, biochemistry & molecular biology, microbiology and parasitology into a single academic unit. SCMB is situated in the beautiful St. Lucia campus on the Brisbane River. New state-of-the art facilities for cryo-EM are currently being installed and will be available on-campus later in the year (including CRYO ARM 300 and CRYO ARM 200 JEOL field-emission cryo-electron microscopes with direct electron detectors for single-particle analysis). Facilities for high-throughput crystallization (Mosquito robots, Rock Imagers) and various biophysical techniques (MALS, ITC, SPR etc) are also available on-campus, and there is regular access to the Australian Synchrotron. Brisbane is one of Australia's most liveable cities and has a fantastic subtropical climate. It is only a short drive from Australia's best beaches and provides opportunities for all sorts of outdoors and cultural activities. The salary will be according to qualifications and experience. The positions are for 2 years, with possible extension subject to funds. The starting date is flexible. The application deadline is 10 May 2019. Please see the links below for details of the positions and application procedures. UQ Jobs: http://jobs.uq.edu.au/caw/en/job/507354/postdoctoral-research-fellowresearch-fellow Seek: https://www.seek.com.au/job/38805305?searchrequesttoken=f7a8a442-55ba-4a76-8db1-854af5090694=standard Please contact Bostjan Kobe (telephone: +617-3365-2132, email b.k...@uq.edu.au<mailto:b.k...@uq.edu.au>) for further information. -- Bostjan Kobe FAA NHMRC Principal Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] database of crystallization condition
Hena I agree with the responses so far, but I think It may not be a complete waste of time looking at the crystallization conditions for similar proteins, you may find a common additive for example and there may be a functional reason for this being required in crystallization. Bostjan --- Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. From: Segelke, Brent W. segel...@llnl.govmailto:segel...@llnl.gov Reply-To: Segelke, Brent W. segel...@llnl.govmailto:segel...@llnl.gov Date: Wed, 24 Jul 2013 16:52:35 + To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] database of crystallization condition Hena, I think this notion of fold families having similar crystallization conditions has been kicking around since the 80’s at least. I seem to recall Gary Gilliland presenting a fairly comprehensive and well controlled study for myoglobins and showing some correlation of crystallization conditions. However, I believe this example is an exception. Just to add to what Janet and Enrico have said: Taking the HIV integrase example from David Davies; or any of the Derewenda surface entropy reduction, protein engineering, examples; it is clear that small changes (even single point mutations) can dramatically alter the bulk properties (and crystallization behavior) of a protein. One last point, it is very hard to control for investigator preference when probing a database of successes. It may be that a review of the BMCD will reveal a correlation between crystallization conditions and fold families, but that could be due to a preference for particular crystallization conditions used in crystallization screens rather than properties of the protein family. Brent Brent W. Segelke Senior Biomedical Scientist Lawrence Livermore National Laboratory 7000 East Avenue, Livermore CA, 94550 USA segek...@llnl.govmailto:segek...@llnl.gov From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Janet Newman Sent: Wednesday, July 24, 2013 9:23 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] database of crystallization condition Dear Hena, The BMCD might be a resource worth investigating: http://xpdb.nist.gov:8060/BMCD4/index.faces Although there are claims that structurally similar proteins may crystallise under similar conditions (the existence of directed screens -such as the Jena Biosciences 'Kinase' screen, you have to wonder (as Enrico points out) how these can work, as the bits that change the most in any protein family are the outside bits (ie, away from the active site) and thus are generally the parts going to affect crystallisation the most. Janet Janet Newman Principal Scientist / Director, Collaborative Crystallisation Centre CSIRO Material Science and Engineering 343 Royal Parade Parkville. VIC. 3052 Australia Tel +613 9662 7326 Email janet.new...@csiro.aumailto:janet.new...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] on behalf of Hena Dutta [hdutt...@gmail.commailto:hdutt...@gmail.com] Sent: 25 July 2013 00:36 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] database of crystallization condition Hi, Can anyone tell, if there is any database containing the crystallization conditions of published structures? I want to see the conditions people have used for those proteins having some structural similarity. Any suggestion would be appreciated. Regards... Hena
Re: [ccp4bb] Maltose binding protein as a tag
Dear Kostas There is a chance your protein is not properly folded by is solubilized by the large MBP tag, and this may be the reason for aggregation. Bostjan --- Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. From: Gang Dong gang.d...@univie.ac.atmailto:gang.d...@univie.ac.at Reply-To: Gang Dong gang.d...@univie.ac.atmailto:gang.d...@univie.ac.at Date: Wed, 24 Jul 2013 18:53:27 +0200 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Maltose binding protein as a tag Dear Kostas, MBP by itself is a monomer. In most of our cases using it as a fusion tag, the yield of a target protein increases drastically (i.e. 5 to 20 folds more). However, we have seen in a couple of cases that the target proteins strongly interact with the MBP tag, which causes oligomerization of the fusion protein. To check whether you have encountered a similar issue, you can try to cut the tag off and check whether your protein still sticks to MBP. Good luck, Gang From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Konstantinos Paraskevopoulos Sent: Wednesday, July 24, 2013 3:07 PM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Maltose binding protein as a tag Dear all, I would like to ask if someone has experience with maltose binding protein (MBP) as a tag. My protein fused to MBP seems to form oligomers that I find difficult to prevent and I was wondering if mbp behaves similar to gst and may also be prone to dimerisation/oligomerisation Many thanks in advance Kostas Paraskevopoulos Research fellow University of edinburgh
Re: [ccp4bb] Efficient way of showing residue conservation
Consurf will do this for you. Bostjan --- Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. On 8/12/11 3:26 PM, Yuri Pompeu yuri.pom...@ufl.edu wrote: I once saw a figure showing the protein as surface, but instead of having it coloured by atom type or potential, it was shown by percent conservation in the family. Something like red highly conserved, all the way to white, not conserved at all... Now, I assume the figure was done by uploading aligned sequnces of several members of a family, and the colouring the generated surface accordingly. Does anyone know a way to do this more elegantly than what I tried doing? ps. I quit colouring them manually after I remebered my protein was 407 aa long...
Re: [ccp4bb] Biological assembly
On 19/10/11 9:19 PM, eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.uk wrote: In case when ASU has the same multiplicity (number of chains) as the probable biological assembly, the latter is an ASU as well. In such a case, the PDB suggests to choose ASU in the form of that assembly, purely for simplicity. It seems to me that this is not an unreasonable suggestion and it would be nice if that were a common practice. Maybe I am misunderstanding what you are saying Eugene, but the ASU interface may not necessarily be the biological interface. I think it is perfectly possible that two subunits in a biological dimer, for example, may be related by crystallographic axis, but the NCS may be a different non-physiological crystal contact, therefore the ASU won't be the same as the biological dimer. So I am not sure if the above applies in general. Bostjan Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
[ccp4bb] Postdoctoral position in Brisbane Australia
Sorry for posting this again, but the web address of the full ad (see below) has changed. The deadline is 10 January. Happy New Year! POSTDOCTORAL POSITION IN MACROMOLECULAR CRYSTALLOGRAPHY, UNIVERSITY OF QUEENSLAND, BRISBANE, AUSTRALIA Applications are invited for a post-doctoral position in macromolecular crystallography in the laboratory of Prof Bostjan Kobe at the School of Chemistry and Molecular Biosciences (SCMB) and the Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Australia. The main area of study will involve characterization of three-dimensional structures of proteins and protein complexes involved in innate immunity pathways. Experience in molecular biology, protein purification, macromolecular crystallography and protein/protein interaction analysis is desirable. The salary will be according to qualifications and experience, starting at AUD$67,958. The position is available from January 2011. University of Queensland is one of Australia's top universities. SCMB combines the disciplines of chemistry, biochemistry molecular biology, microbiology and parasitology into a single academic unit. The laboratory is located in a recently refurbished area of SCMB. SCMB and IMB are situated in the beautiful St. Lucia campus on the Brisbane River. State-of-the art equipment is available for all aspects of the work, including FR-E X-ray generator /R-axis IV++ and Saturn 944 CCD X-ray detectors, Mosquito crystallization robot and the Rock Imager imaging system. There is regular access to the Australian Synchrotron. Brisbane has been voted Australia's most liveable city and has a fantastic subtropical climate. It is only a short drive from Australia's best beaches and provides opportunities for all sorts of outdoors and cultural activities. For further information please see http://www.seek.com.au/Job/postdoctoral-research-fellow/in/brisbane/18804467 or contact Bostjan Kobe (telephone: +617-3365-2132, email b.k...@uq.edu.au). Please forward applications, including a cover letter, curriculum vitae and contact details for three referees, by by 10 January 2011, to Bostjan Kobe by email (b.k...@uq.edu.au) or post (Bostjan Kobe, SCMB, University of Queensland, St. Lucia, Queensland 4072, Australia). --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
Re: [ccp4bb] Structure containing nickel ions from Ni-NTA column
Hi Kristof We had an example a few years back, with a Co ion leakage off an old Talon resin necessary for the crystal to grow (until we realized you could just add Co instead to get crystals to grow). The ion was used in the end as anomalous scatterer to solve the structure, and was found bound nicely between two molecules in the crystal. Guncar et al, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Mar 1;63(Pt 3):209-13 http://www.ncbi.nlm.nih.gov/pubmed/17329816 Bostjan On 10/12/10 9:17 PM, Kristof Van Hecke kristof.vanhe...@chem.kuleuven.be wrote: Dear, I was wondering if anybody has experienced before the leakage of Ni-ions (from a Ni-NTA column) and additionally binding to specific sites in the protein structure..? Many thanks Regards Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327477 -- --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
[ccp4bb] Postdoctoral position in Brisbane Australia
POSTDOCTORAL POSITION IN MACROMOLECULAR CRYSTALLOGRAPHY, UNIVERSITY OF QUEENSLAND, BRISBANE, AUSTRALIA Applications are invited for a post-doctoral position in macromolecular crystallography in the laboratory of Prof Bostjan Kobe at the School of Chemistry and Molecular Biosciences (SCMB) and the Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Australia. The main area of study will involve characterization of three-dimensional structures of proteins and protein complexes involved in innate immunity pathways. Experience in molecular biology, protein purification, macromolecular crystallography and protein/protein interaction analysis is desirable. The salary will be according to qualifications and experience, starting at AUD$67,958. The position is available from January 2011. University of Queensland is one of Australia's top universities. SCMB combines the disciplines of chemistry, biochemistry molecular biology, microbiology and parasitology into a single academic unit. The laboratory is located in a recently refurbished area of SCMB. SCMB and IMB are situated in the beautiful St. Lucia campus on the Brisbane River. State-of-the art equipment is available for all aspects of the work, including FR-E X-ray generator /R-axis IV++ and Saturn 944 CCD X-ray detectors, Mosquito crystallization robot and the Rock Imager imaging system. There is regular access to the Australian Synchrotron. Brisbane has been voted Australia's most liveable city and has a fantastic subtropical climate. It is only a short drive from Australia's best beaches and provides opportunities for all sorts of outdoors and cultural activities. For further information please see http://www.seek.com.au/Job/postdoctoral-research-fellow/in/brisbane/18662165 , or contact Bostjan Kobe (telephone: +617-3365-2132, email b.k...@uq.edu.au). Please forward applications, including a cover letter, curriculum vitae and contact details for three referees, by by 10 January 2011, to Bostjan Kobe by email (b.k...@uq.edu.au) or post (Bostjan Kobe, SCMB, University of Queensland, St. Lucia, Queensland 4072, Australia). --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
Re: [ccp4bb] monomer-dimer
Dear Intekhab Let me just add to this that gel filtration is not an accurate method for determination of molecular mass, because the migration on the column depends on the shape of the protein. The following methods can be used to determine molecular mass irrespective of shape: - MALLS (multi-angle laser light scattering or static light sxattering) - sedimentation equilibrium on analytical ultracentrifuge (AUC) - native mass spectrometry For a short recent review on issues associated with determining oligomeric state from crystal structures, with older references and relevant bioinformatic tools cited in there, please see http://www.ncbi.nlm.nih.gov/pubmed/19021571 Bostjan On 10/08/10 6:26 AM, Maia Cherney ch...@ualberta.ca wrote: To determine the oligomeric state of a protein (monomer or dimer in your case), it's useful to use the PISA server. You upload your pdb file from the crystal structure.The server calculates the areas of interfaces (buried area) and deltaG (change in Gibbs energy) upon oligomer dissociation. (E. Krissinel and K. Henrick (2007). /Inference of macromolecular assemblies from crystalline state/. J. Mol. Biol. *372*, 774--797 . E. Krissinel and K. Henrick (2005). /Detection of Protein Assemblies in Crystals/. In: M.R. Berthold /et.al./ (Eds.): CompLife 2005, LNBI 3695, pp. 163--174 http://dx.doi.org/10.1007/11560500_15. E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. J. Comp. Chem., in press; published on-line 6 May 2009; DOI 10.1002/jcc.21303} If the interface area (divided by 2 per one protomer) is greater than 1000 A2 and delta G is more than 5kcal/mol (the higher the better), it's a dimer. However, don't forget that most dimers can dissociate into monomers upon dilution. There is a dynamic equilibrium between dimers (oligomers) and monomers that depends on their concentration and the Kdiss. Separating them in any method will disturb this equilibrium. If the re-equilibration time is greater than the separation time, you can see both monomers and dimers. You can even roughly calculate the dissociation constant: Kdiss=[monomer]2/[dimer] where brackets mean concentrations. To give you an estimate, at Kdiss=10(-3)M, you have roughly equal concentration of dimers and monomers at 10-3 M and only 10% dimers at 10-4 M. Sometimes, protein needs to dissociate easily for the biological function. Maia intekhab alam wrote: Hi everyone Sorry for some non specific query! i am working with a protein that shows a dimer in the crystal structure but when i tried to figure out that with standard molecular markers in gel filteration (superdex-200, 24ml column) it turned out to be a monnomer. Native gel analysis after incubating the protein at 20 degree, 37 degree showed more dimer at 20 degree celcius as compared to 37. I tried similar strategy in gel filteration by incubating my protein at various temperature,where a lot of precipitation was observed at 37 degree celcius and after removing the precipitates i run the gel filteration that has 0.5 ml higher elution volume as compared to samples incubated at 20 degree celcius and 4 degree celcius.( Is this significant) Furthermore i have done some experiments in cold room (4 degree) where the elution volume is stuck at a point irrespective of the conditions (as Flow rate, concentration of protein etc) and that is higher than that of the room temperature by 1 ml. Standard moleculr weight markers also show higher elution volume in cold room in comparison to the room temperature by 1 ml. I will be highly obliged if someone suggest some literature or any otherway to do gel filtrtaion so that i can clearly resolve this issue. Also let me know if there is some literature available on effect of temperature on the elution volume of proteins. Thanks in advance -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
Re: [ccp4bb] crystal contacts
Dear Amit As Paul suggests, you can get some idea if the interaction is consistent with biologically relevant protein-protein interfaces through looking at the the size of the interface and the nature of the contacts in the interface. There is substantial literature on this topic, see http://www.ncbi.nlm.nih.gov/pubmed/19021571?itool=EntrezSystem2.PEntrez.Pubm ed.Pubmed_ResultsPanel.Pubmed_RVDocSumordinalpos=11 for example for a review. The better way of course to test the relevance of this interface is experimentally, by mutating the tyrosines and seeing the effect on the oligomeric state in solution. Best wishes Bostjan On 23/02/10 12:57 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: amit sharma wrote: Apologies for a non-CCP4question. Aggh! Stop! Stop it! Stop apologising for using CCP4BB in the way it is supposed to be used! And not only that, this is not a non-CCP4 question. I have a structure of a dimeric molecule, where the interfaces between monomers is held by a couple of tyrosine residues (per monomer) juxtaposed with each other. The molecule exists as a dimer in solution. Are there ways/programs to show that the interaction between the tyrosine residues is not a consequence of crystal contacts. I guess the fact that the molecule occurs as a dimer in solution strongly suggests so. Also, any directions towards literature showing similar cases would be of great help. PISA tries to distinguish between assemblies that occur only as a result of crystal contacts and those that are intrinsic molecular interactions. Paul. --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
Re: [ccp4bb] unknown density
I think there is at least one more option here (relevant at least in some rare cases): Identifying what that something is likely to be can be significant and may advance your career Of course it is important to present supporting or otherwise evidence for the interpretation. As already discussed, this is difficult in a PDB file, and that¹s why the accompanying publication can be very important. Bostjan On 4/02/10 3:54 AM, Bernhard Rupp b...@ruppweb.org wrote: General remark if I may Putting nothing in: no significant effect on model and life in general Putting something¹ potentially wrong and misleading in: could be detrimental to your career BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Katja Schleider Sent: Wednesday, February 03, 2010 9:18 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unknown density Dear all, I found some fairly substantial density in the active site of my protein structure. But I don´t know what it should be. My crystallisation condition consists of lithium sulfate, citrate-phosphate and peg1000. The whole lot doesn't make a dashed bit of sense! Any suggestions to fill this density with something? Picture is attached. Thanks a lot, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
[ccp4bb] Postdoctoral position in Brisbane, Australia
Happy New Year everyone Sorry for posting this again, but the application deadline is 18 January (still 2 weeks away) and it has been a while since I posted this the first time. Thanks to everyone who applied already! POSTDOCTORAL POSITION IN MACROMOLECULAR CRYSTALLOGRAPHY, UNIVERSITY OF QUEENSLAND, BRISBANE, AUSTRALIA Applications are invited for two macromolecular crystallography post-doctoral positions in the laboratory of Prof Bostjan Kobe at the School of Chemistry and Molecular Biosciences (SCMB) and the Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Australia. The main area of study will involve characterization of three-dimensional structures of proteins and protein complexes involved in the process of bacterial pathogenesis, in a collaborative project involving several other groups at the University of Queensland, Griffith University and University of Adelaide. Experience in molecular biology, protein purification, macromolecular crystallography and protein/protein interaction analysis is desirable. The salary will be according to qualifications and experience, starting at AUD$62,807. The position is available from January 2010. University of Queensland is one of Australia's top universities. SCMB combines the disciplines of chemistry, biochemistry molecular biology, microbiology and parasitology into a single academic unit. The laboratory is located in a recently refurbished area of SCMB. SCMB and IMB are situated in the beautiful St. Lucia campus on the Brisbane River. State-of-the art equipment is available for all aspects of the work, including FR-E X-ray generator /R-axis IV++ and Saturn 944 CCD X-ray detectors, Mosquito crystallization robot and the Rock Imager imaging system. Brisbane has been voted Australia's most liveable city and has a great subtropical climate. It is only a short drive from Australia's best beaches and provides opportunities for all sorts of outdoors and cultural activities. For further information please see http://www.seek.com.au/job/postdoctoral-research-fellow/brisbane/16371465/99 /1/ or contact Bostjan Kobe (telephone: +617-3365-2132, email b.k...@uq.edu.au). Please forward applications, including a cover letter, curriculum vitae and contact details for three referees, by email or post to by 18 January 2010 to Bostjan Kobe, SCMB, University of Queensland, St. Lucia, Queensland 4072, Australia. --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. -- End of Forwarded Message
Re: [ccp4bb] Hanging vs. Sitting
There is really not much difference in terms of setup between hanging and sitting drop, especially if the drops are set up on tape. Visualization is also usually easier with hanging drops. Bostjan On 1/05/09 1:37 AM, Poul Nissen p...@mb.au.dk wrote: We often find results to be very different between hanging and sitting drops (equilibration kinetics for one may be the explanation). Then there's the good thing of hanging drops that crystals rarely stick to the surface of the support facilitating the mounting procedure, in particular for fragile crystals. All in all we much prefer hanging drops for our membrane proteins - the bottle neck is not in the extra few minutes for set-up, but in the months it takes to produce the protein. Poul On 30/04/2009, at 16.45, Jacob Keller wrote: I have noticed that a significant majority of crystallizations are done in hanging- rather than sitting-drop configuration, and considering the significant extra labor involved in hanging drops, can only understand this preference as a historical bias. I understand that sometimes one technique works and not the other, but all things being equal, why is hanging drop still hanging around? Any insights appreciated... Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 452 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
[ccp4bb] Postdoctoral position at the University of Queensland, Brisbane, Australia
Sorry for posting this ad again, but for some reason the University has changed the address of the web advertisement. The applications are still open, the deadline is 16 January. POST-DOCTORAL POSITION IN PROTEIN CRYSTALLOGRAPHY, THE UNIVERSITY OF QUEENSLAND, BRISBANE, AUSTRALIA Applications are invited for a protein crystallography post-doctoral position in the laboratory of Prof Bostjan Kobe at the School of Molecular and Microbial Sciences (SMMS) and the Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Australia. The main area of study will involve the characterization of structures and interactions of proteins involved in the process of plant disease resistance, focusing on flax-flax rust host-pathogen interaction as the model system (for recent publications in this area see Dodds PN et al (2006) Proc Natl Acad Sci USA 103: and Wang C-IA et al (2007) Plant Cell 19: 2898). Experience in molecular biology, protein purification, protein/protein interaction analysis and protein crystallography is desirable. The salary will be according to qualifications and experience, starting at AUD$ $73,484. The position is available from January 2009. University of Queensland is one of Australia's top universities. SMMS combines the disciplines of chemistry, biochemistry molecular biology, microbiology and parasitology into a single academic unit. SMMS and IMB are situated in the beautiful St. Lucia campus on the Brisbane River. State-of-the art equipment is available for all aspects of the work, including FR-E X-ray generator /R-axis IV++ and Saturn 944 CCD X-ray detectors, Mosquito crystallization robot and the Rock Imager imaging system. Brisbane has been voted Australia's most liveable city and has a great subtropical climate. It is only a short drive from Australia's best beaches and provides opportunities for all sorts of outdoors and cultural activities. For further information please see http://seek.com.au/users/apply/index.ascx?Sequence=96PageNumber=1JobID=147 05860 or contact Bostjan Kobe (telephone: +617-3365-2132, email b.k...@uq.edu.au). Please forward applications, including a cover letter, curriculum vitae and contact details for three referees, by email or post to by 16 January 2008 to Bostjan Kobe, SMMS, University of Queensland, St. Lucia, Queensland 4072, Australia. --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 452 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
Re: [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer?
I wanted to comment on a couple of things that came up during this discussion. 1. We use crystallography because it enables us to get structural information. But we have to be aware that most of the time a crystal will not be an exact reflection of the biological environment, which is usually what we want to relate our structure to. For this reason, to make any useful interpretations of the oligomeric state and how it relates to a biologically relevant situation, one needs to complement it with other studies (hopefully in a solution that better resembles the biological situation). 2. What you find in the asymmetric unit of a crystal does not necessarily have anything to do with the biologically relevant oligomeric state (biological unit). I commonly see researchers confuse the asymmetric unit with the biological unit, even in submitted and published papers. To phrase it in a different way, crystallographic symmetry often relate subunits in an oligomer, and conversely NCS often corresponds to just another biologically irrelevant crystal contact. 3. It is often not trivial to distinguish crystal contact from the oligomeric interface. There is lots of literature on this, and software and databases that can help you distinguish between these (using the size of interface area, but also many other criteria to sort these interactions). It is often not going to be possible to do so with any high reliability without complementary experiments. Please refer to the references cited in this recent conference proceeding for extensive literature on this matter: http://www.ncbi.nlm.nih.gov/pubmed/19021571?ordinalpos=1itool=EntrezSystem2 .PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSu m. Best wishes Bostjan On 12/12/08 2:34 AM, Ethan A Merritt merr...@u.washington.edu wrote: On Thursday 11 December 2008, Santarsiero, Bernard D. wrote: In parallel with the discussion around this off-CCP4-topic, are they any good examples of the opposite case, where the protein is a monomer in solution (as evident from light scattering, MW determination through centrifugation, EPR, etc.) but crystallizes as a dimer or higher multimer? I don't think such a question is entirely well-defined, for two reasons. 1) The monomer/dimer equilibrium in solution may well depend on the specific conditions (pH, concentration, presence of ligands, temperature, etc). Unless these conditions are replicated in your crystallization medium, it is uncertain to what extent the solution measurement is relevant. 2) How extensive an interface is required in order for it to be considered a dimer/multimer interaction? In the limiting case of very small interfaces, the entire crystal might be consider a single oligomer, with each lattice-packing contact constituting a monomer:monomer interaction. That's not a very useful place to set the threshold, but where do you set it - 100 A^2 ? 500 A^2 ? 1000 A^2? Some definition other than surface area? That said, I have some interest in the question as a practical matter. We have a new structure that is obviously, but totally unexpectedly, a tetramer in the crystal. In this case the monomer:monomer interaction surface is 1500 A^2. But exactly what criteria would I use to argue that this is a real tetramer? What criteria would I use to argue that it is a crystal artifact? Yes, of course ideally one would go back to the lab and survey for solution measurements that are consistent with tetramerization, but that is not always practical, and may lead right back to your original question. --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 452 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
Re: [ccp4bb] His tag
Dear Yanming Lots of proteins have been crystallized with His-tags on. However, in general one would assume that a flexible tag could have a negative effect. I am not aware of a systematic comparison of crystallization of tagged and untagged proteins, but the following paper is relevant to this topic: Carson M, Johnson DH, McDonald H, Brouillette C, Delucas LJ. His-tag impact on structure. Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):295-301. Epub 2007 Feb 21. PMID: 17327666 [PubMed - indexed for MEDLINE] I would expect the same protein with the tags on different ends would often crystallize under similar conditions, as long as the tags do not interfere with the packing in the crystal. Bostjan On 5/2/08 11:54 AM, Yanming Zhang [EMAIL PROTECTED] wrote: Hi All, Maybe, I should not have asked this question: Can anybody give me the hints (or point to the references) on the impact of His tag on crystallization experiments. In perticular: 1, With or without His tag, which one is better for crystallization? 2, If I successfully crystallized N-terminal, what information can I get to assist my set-up of C-terminal crystallization set-up. Sorry for taking up your time because of my inadequate knowledge Thank you for your help Yanming --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Molecular and Microbial Sciences and Institute for Molecular Bioscience Office: Building 76 Room 452 Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: [EMAIL PROTECTED] URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
[ccp4bb] Post-doctoral positions in protein crystallography, University of Queensland, Brisbane, Australia
POST-DOCTORAL POSITIONS IN PROTEIN CRYSTALLOGRAPHY, UNIVERSITY OF QUEENSLAND, BRISBANE, AUSTRALIA Applications are invited for two protein crystallography post-doctoral positions in the laboratory of Prof Bostjan Kobe at the School of Molecular and Microbial Sciences (SMMS) and the Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Australia. The main area of study will involve the structural and functional characterization of proteins and protein-protein complexes from macrophages, cells with important roles in the immune response and chronic inflammatory diseases. Experience in molecular biology, protein purification, protein/protein interaction analysis and protein crystallography is desirable. The salary will be according to qualifications and experience, starting at AUD$68,600. The positions are available immediately. University of Queensland is one of Australia's top universities. SMMS combines the disciplines of chemistry, biochemistry molecular biology, microbiology and parasitology into a single academic unit. SMMS and IMB are situated in the beautiful St. Lucia campus on the Brisbane River. State-of-the art equipment is available for all aspects of the work, including FR-E X-ray generator /R-axis IV++ and Saturn 944 CCD X-ray detectors, Mosquito crystallization robot and the Rock Imager imaging system. Brisbane has been voted Australia's most liveable city and has a great subtropical climate. It is only a short drive from Australia's best beaches and provides opportunities for all sorts of outdoors and cultural activities. For further information please see http://seek.com.au/users/apply/index.ascx?JobID=10855313 or contact Bostjan Kobe (telephone: +617-3365-2132, email [EMAIL PROTECTED]). Please forward applications, including a curriculum vitae and contact details for three referees, by email or post to by 16 November 2007 to Bostjan Kobe, SMMS, University of Queensland, St. Lucia, Queensland 4072, Australia. --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Molecular and Microbial Sciences and Institute for Molecular Bioscience Office: Building 76 Room 452 Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: [EMAIL PROTECTED] URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
