[ccp4bb] Marsden Funded PhD Project Available (New Zealand)
Hi, I am looking for a suitable student for a PhD project we have on offer and thought this might be the perfect place to find a suitably experienced candidate. The project (Understanding protein communication networks) will involve a range of techniques (structural biology/protein chemistry/molecular biology) so a candidate with interest in proteins and some experience in these areas would be ideal. The project is funded by funded by the Royal Society Te Apārangi Marsden Fund and full details of the project can be found at this link: https://www.findaphd.com/search/ProjectDetails.aspx?PJID=95088 The project would be based in New Zealand; primarily at the Biomolecular Interaction Centre (http://www.canterbury.ac.nz/bic/) at the University of Canterbury, with some work carried out at the University of Auckland. So if you would like to know more, or know of anyone who is interested/suitable and eager to come to NZ we are keen to hear from you. Thanks. Jodie -- Dr Jodie Johnston Senior Lecturer Department of Chemical and Physical Sciences University of Canterbury Christchurch New Zealand e-mail: jodie.johns...@canterbury.ac.nz This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information.
Re: [ccp4bb] I222 - P22121 space-group ambiguity
Hi Florian, Not sure if this is helpful or not but I have a particular protein that seems to be either P22121 (with 2 molecules) or I222 (with one molecule). Not from the same drop but crystallised in similar conditions but with different small molecules bound. In many cases the crystals can be processed in both space groups but refine better in one over the other. I always thought (as the small molecules affect some loops folding on the active site in my case) that sometimes all my protein molecules had the same conformation of those loops and in other cases there were subtle differences - do you see any differences or small molecules bound asymmetrically in your P22121 cases ? Best regards Jodie From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Florian Schmitzberger [schmitzber...@crystal.harvard.edu] Sent: Monday, 13 October 2014 9:47 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] I222 - P22121 space-group ambiguity Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the ‘true’ space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It’s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?
Thanks Everyone for your input I shall triple check my reasoning tomorrow and email Garib if I do think there is an issue. Thanks Jodie From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson [eleanor.dod...@york.ac.uk] Sent: Tuesday, 29 October 2013 11:51 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ? There are errors in every branch of human endeavour I am sure! Please if you find something wrong. send your suggested correction to Garib & Paul, and once there is a fix notify us all via the BB. CCP4 has always depended heavily on the users noticing the bugs Thank you for your observation. Eleanor On 29 October 2013 10:21, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Jodie, > > except for the matter if there is 'right' and 'wrong' in science or > rather 'good' and 'bad' models, Garib Murshudov maintains the > cif-library and if you send him a compilation of possible fixes he > would surely appreciate your input. > > Best, > Tim > > On 10/29/2013 10:15 AM, Jodie Johnston wrote: >> Hi >> >> >> >> I wanted to check is it possible that there could >> >> be errors in the library cif files associated with CCP4 and coot ? >> >> I have noticed a couple of potential errors in a ligand cif file >> from the CCP4 library. >> >> >> >> Perhaps it is my error - I shall need to triple check it again but, >> if it appears not to be, is it possible >> >> to talk to someone about correcting the cif file ? >> >> >> >> >> >> Many Thanks >> >> >> >> Jodie >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.15 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFSb4wRUxlJ7aRr7hoRAu21AJ9u78CgI0EV2shsvQS7ghl1FbddxwCgjxfJ > EfmUgIVb9xKGdzmxSaRsBbw= > =7+vC > -END PGP SIGNATURE-
[ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?
Hi I wanted to check is it possible that there could be errors in the library cif files associated with CCP4 and coot ? I have noticed a couple of potential errors in a ligand cif file from the CCP4 library. Perhaps it is my error - I shall need to triple check it again but, if it appears not to be, is it possible to talk to someone about correcting the cif file ? Many Thanks Jodie
Re: [ccp4bb] Off topic: His-tag purification
Hi Theresa, I am right in thinking the protein construct you are using is just 8 His residues added to 90kDa ? It could be (if this is the case) that the tag is not accessible for binding to the Ni column. Sometimes you need a linker sequence between the protein for the His-tag to coordinate well to the Ni2+. Hope that helps Cheers Jodie From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Theresa H. Hsu [theresah...@live.com] Sent: Monday, 16 January 2012 7:23 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off topic: His-tag purification Hi all I have a His-tagged soluble protein (8 His residues added to 90 kDa protein) that do not bind to IMAC column based on flowthrough showing up with Western blott. Do you have suggestions to improve the binding? Binding condition is 50 mM Tris-HCl 8.0, 300 mM NaCl, 10 mM imidazole pH to 8.0. Thank you. Theresa
