Re: [ccp4bb] unknown density in 1.6 A structure
Dear Nick, I like your idea and your comments on this substance. 1,2-hexandiol supposed to be chiral but probably it is used as a racemic mixture in cosmetics. There is even a crystal structure in the PDB (4EUS) and an associated 3 letter code. I´ll give it a try because it seems to fit nicely the ED map. I just have to find out how to handle racemics in buster refinement. Thank you all for your helpful comments. Have a nice day. -Peer Am 03.06.2021 um 13:00 schrieb Nicholas Keep: How about an overlay of the structure you have with a second ligand conformation where the OH and CH2OH are swapped? ie two alternative conformations of the ligand. That might remove the last green density 1,2-hexanediol is apparently widely used in cosmetics and moisturisers. Did someone somehow touch the protein or crystallisation tray with recently moisturised hands? Even so it must have very high affinity for your protein Best wishes Nick 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/
Re: [ccp4bb] unknown density in 1.6 A structure
Hi Peer, Reminds me of a lipocalin structure I solved which co-purified fatty acid with it. I could model fatty acids and we along with our collaborators used several complementary biophysical methods followed by functional assays to identify the ligand. https://www.sciencedirect.com/science/article/abs/pii/S002228360901078X [https://ars.els-cdn.com/content/image/1-s2.0-S0022283609X00422-cov150h.gif]<https://www.sciencedirect.com/science/article/abs/pii/S002228360901078X> Serendipitous Fatty Acid Binding Reveals the Structural Determinants for Ligand Recognition in Apolipoprotein M<https://www.sciencedirect.com/science/article/abs/pii/S002228360901078X> Apolipoprotein M (ApoM) is a 25-kDa HDL-associated apolipoprotein and a member of the lipocalin family of proteins. Mature apoM retains its signal pep… www.sciencedirect.com Thank you. All the best, Madhu Madhumati Sevvana, Ph.D. Assistant Research Scientist Structural Virology lab of Prof. Richard Kuhn Hockmeyer Hall of Structural Biology Department of Biological Sciences Purdue University, West Lafayette IN From: CCP4 bulletin board on behalf of Peer Mittl Sent: Thursday, June 3, 2021 06:50 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unknown density in 1.6 A structure I'm struggling with the electron density shown in the attachment. The substance does not seem to come from the crystallization condition nor from the mounting buffer. The 1.6 A maps are rather clear, because the compound binds into the hydrophobic core, which seems to be loosely packed. -Peer 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, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] unknown density in 1.6 A structure
Dear Peer, This reminds me of my colleague Michael Rossmann's discovery of a Pocket Factor which is a fatty acid-like molecule residing in a hydrophobic pocket underneath the "canyon" in enteroviruses. See https://link.springer.com/article/10.1007/s13238-014-0092-6. You likely have an endogenous ligand that binds and stays bound during purification. You may want to do some MS on your purified protein to see if you can identify it. Your density should provide enough information on a mass range to look for. Andy Mesecar On Thu, Jun 3, 2021 at 6:50 AM Peer Mittl wrote: > I'm struggling with the electron density shown in the attachment. The > substance does not seem to come from the crystallization condition nor > from the mounting buffer. The 1.6 A maps are rather clear, because the > compound binds into the hydrophobic core, which seems to be loosely packed. > > -Peer > > > > > > 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/ > -- *Andrew D. Me**secar* Head, Department of Biochemistry Walther Professor of Cancer Structural Biology Deputy Director, Purdue Center for Cancer Research E-Mail: amese...@purdue.edu _ *Department of Biochemistry Contact Information:* 175 S. University Street W. Lafayette, IN 47907-2063 765-494-1607 -- *Research Lab Contact Information:* Hockmeyer Hall of Structural Biology Room 311 240 S. Martin Jischke Drive West Lafayette, IN 47907-1971 765-494-1924 _ 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/
[ccp4bb] AW: [ccp4bb] unknown density in 1.6 A structure
Hi Peer, this density reminds me of something I saw in one of my own structures as well and which also was not a component that should have been in there (PDB ID 6SMT). I never truly found out what it was, but I modeled it as 2-ethylhexanol, which is known to be a precursor for the synthesis and also degradation product of the wide-spread plasticizer DEHP, although I found out, that at least our crystallization plates do not contain this component. Best, Timo Von: CCP4 bulletin board im Auftrag von Peer Mittl Gesendet: Donnerstag, 3. Juni 2021 12:50:00 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] unknown density in 1.6 A structure I'm struggling with the electron density shown in the attachment. The substance does not seem to come from the crystallization condition nor from the mounting buffer. The 1.6 A maps are rather clear, because the compound binds into the hydrophobic core, which seems to be loosely packed. -Peer 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, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] unknown density in 1.6 A structure
Hi Peer, If I understand you correctly you are saying that you do not know what substance may be in the density; then perhaps you only need to extend by an extra atom to create a new kind of symmetrical molecule that will fit the density? BW, D On 03/06/2021 11:55, SHEPARD William wrote: Hi Peer, Have you tried to model the hydroxyl O1 disordered at the carbonyl position? Check the H-bonding pattern to the end groups, this might give some clues. Cheers, Bill Le 03/06/21 12:50, « Peer Mittl » a écrit : I'm struggling with the electron density shown in the attachment. The substance does not seem to come from the crystallization condition nor >from the mounting buffer. The 1.6 A maps are rather clear, because the compound binds into the hydrophobic core, which seems to be loosely packed. -Peer 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/ 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/ -- Dom Bellini, Xray Crystallography Facility (1S205) MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH Phone 01223 267839 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/
Re: [ccp4bb] unknown density in 1.6 A structure
Hi Peer, Have you tried to model the hydroxyl O1 disordered at the carbonyl position? Check the H-bonding pattern to the end groups, this might give some clues. Cheers, Bill Le 03/06/21 12:50, « Peer Mittl » a écrit : >I'm struggling with the electron density shown in the attachment. The >substance does not seem to come from the crystallization condition nor >from the mounting buffer. The 1.6 A maps are rather clear, because the >compound binds into the hydrophobic core, which seems to be loosely >packed. > >-Peer > > > > > >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/ 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/