Subject: Re: High-order oligomers vs robust crystals - references? Hi Frank et al. Joining the discussion at this humorous stage...
What about Janin's contributions on crystal packing versus oligomer interfaces? There are useful ideas in this assessment: https://www.cambridge.org/core/journals/quarterly-reviews-of-biophysics/article/abs/proteinprotein-interaction-and-quaternary-structure/670665304EE0AFE280652CCBBA3F55D1 Peter _____________________________________________ Peter Crowley PhD Professor (Protein Chemistry) School of Chemistry Orbsen Building National University of Ireland, Galway University Road Galway Ireland Ph: + 353 91 49 24 80 http://www.nuigalway.ie/our-research/people/chemistry/petercrowley/ ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of CCP4BB automatic digest system <lists...@jiscmail.ac.uk> Sent: Thursday, December 2, 2021 12:00 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: CCP4BB Digest - 30 Nov 2021 to 1 Dec 2021 (#2021-335) EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open attachments or click on links in the message unless you recognise the sender's email address and believe the content is safe. RÍOMHPHOST SEACHTRACH: Tháinig an ríomhphost seo as áit éigin taobh amuigh de OÉ Gaillimh. Ná cliceáil ar naisc agus ná hoscail ceangaltáin mura n-aithníonn tú seoladh ríomhphoist an tseoltóra agus mura gcreideann tú go bhfuil an t-ábhar sábháilte. There are 5 messages totaling 677 lines in this issue. Topics of the day: 1. High-order oligomers vs robust crystals - references? 2. Four open postdoc positions @ NIH 3. JCSG structure validation server (3) ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ---------------------------------------------------------------------- Date: Wed, 1 Dec 2021 07:33:20 +0000 From: Frank von Delft <frank.vonde...@cmd.ox.ac.uk> Subject: Re: High-order oligomers vs robust crystals - references? Dear all, thanks all for the several references you emailed around. Here's a summary: A Suite of Engineered GFP Molecules for Oligomeric Scaffolding https://www.sciencedirect.com/science/article/pii/S0969212615002890 Dimerization properties of the RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis https://pubmed.ncbi.nlm.nih.gov/22868772/ An approach to crystallizing proteins by synthetic symmetrization https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1637565/ Why protein crystals favour some space-groups over others https://www.nature.com/articles/nsb1295-1062 Infinite Assembly of Folded Proteins in Evolution, Disease,and Engineering https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201806092 James Holton duly challenged me, and here's my reply: JH: If I told you "no, that's not true", how would you go about proving me wrong? What would that data look like? -- FvD: Geezus, I don't know! It's not me that hurled this brainfart around the grant funding agencies 20 years ago... That's why I asked the Social Brain. But my primary goal was to have something to stick into the introduction to a paper, so that has been achieved. Whether it's ethical to perpetuate a brainfart by citing other expressions of the brainfart is a reasonable question, but this one would rank quite low on the impact-of-transgression scale, methinks. But Dhiraj's reply to my original question is a surely a better one: /"Recently there were few articles where synthetic symmetrization was used to enhance the crystallizability. proteins used were MBP, lysozyme and GFP to name a few."// / It implies the weight-of-evidence is out there - hint to you enterprising students, looking for something *actually useful* to write a review about! Frank On 12/11/2021 14:52, Frank von Delft wrote: > Hello all > > Two decades ago, I remember (!) much talk about a reason that > bacterial proteins crystallize "more easily" is that they tend to come > as oligomers (dimers and up), and that this internal symmetry made > them happier to crystallize. > > Did anybody ever publish hard evidence? Or even, is there a primary > citation for the idea? > > Thanks > Frank > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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&A=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/policyandsec ------------------------------ Date: Wed, 1 Dec 2021 12:53:40 +0000 From: "Elmlund, Hans (NIH/NCI) [E]" <hans.elml...@nih.gov> Subject: Four open postdoc positions @ NIH The Biological Computing Section (BCS) Center for Structural Biology (CSB), National Cancer Institute (NCI)—Frederick campus are seeking to recruit four postdoctoral fellows. Link to ad below: https://ccr.cancer.gov/careers/post-doctoral-fellow-electron-microscopy-image-processing-algorithm-development/24314 The job involves development of algorithmic solutions to address the increasing demands for quantitative and computational approaches in electron microscopy, integrative structural biology, and materials science. The candidate will be working in a creative collaborative team developing and applying novel computational solutions for analyzing high-dimensional noisy image data. -- HANS ELMLUND PhD Senior Investigator National Institutes of Health National Cancer Institute—Frederick Campus 1050 Boyles St, Fredrick MD 21702 United States of America T: +1(301)846-5670 M: +1(240)739-9079 E: hans.elml...@nih.gov<mailto:hans.elml...@nih.gov> simplecryoem.com ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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.jis ------------------------------ Date: Wed, 1 Dec 2021 14:12:38 +0000 From: "Hough, Michael" <maho...@essex.ac.uk> Subject: JCSG structure validation server Hi all, I recently tried to use the structure validation server and found that the web link is no longer active. I wonder if anyone has an idea of whether it is still available elsewhere or whether it has been discontinued? Thanks, Mike ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ Date: Wed, 1 Dec 2021 11:07:22 -0800 From: Debanu Das <debanu....@gmail.com> Subject: Re: JCSG structure validation server Hi Mike, As an ex-JCSG team member, I can verify that the JCSG QC structure validation server (as well as other ones we had), are unfortunately not operational anymore. We are trying to rebuild (and reinvent along the way) some more of the JCSG legacy stuff in our current efforts. Best, Debanu On Wed, Dec 1, 2021 at 6:13 AM Hough, Michael <maho...@essex.ac.uk> wrote: > Hi all, > > > > I recently tried to use the structure validation server and found that the > web link is no longer active. I wonder if anyone has an idea of whether it > is still available elsewhere or whether it has been discontinued? > > > > Thanks, > > > > Mike > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ Date: Wed, 1 Dec 2021 20:05:16 +0000 From: Gye Won Han <gyewon....@usc.edu> Subject: Re: JCSG structure validation server Hi Mike snd Debanu - QC check has been retired from SSRL computer a while ago. We (Bridge Structural Biology Center, USC) is working on installing it in our server for the structural biology community. Our IT specialist, Robin, is in charge of it. If you have any question, please contact him. As far as I know, we are very close to make QC- check revive. We will keep you posted. Thanks, Gye Won ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Hough, Michael <maho...@essex.ac.uk> Sent: Wednesday, December 1, 2021, 6:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] JCSG structure validation server Hi all, I recently tried to use the structure validation server and found that the web link is no longer active. I wonder if anyone has an idea of whether it is still available elsewhere or whether it has been discontinued? Thanks, Mike ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!LIr3w8kk_Xxm!-OJl8IaiBwfBHhcOXcIhHais8R7F5L9UFFFWAsOoT6PCKgx_6z1FlkyHrhGgWv3U0g$> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ End of CCP4BB Digest - 30 Nov 2021 to 1 Dec 2021 (#2021-335) ************************************************************ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
