Re: [ccp4bb] AW: Strange cysteines
Another possibility to model is a couple of S-hydroxy cysteines. We've seen that in a Cys-amidase where there was artifactual oxidation damage to the protein during storage or RT crystallization. Roger Rowlett On Wed, Dec 22, 2021, 8:00 AM Andrew Purkiss wrote: > As you say, the Cys are too far apart for it to be a disulphide and it > looks like oxidation of the Cys. This could be due to radiation > damage, but other causes are possible. > > A former colleague had one in betaB1-crystallin, which is visible in > pdbcode 1OKI at position 38. The difference density was quite clear > before it was modeled as Cysteine sulfinic acid (CSD). Of course, it > was easy to see at 1.4 Angstrom resolution. > > Andy > > Quoting "Hochberg, Georg" : > > > Hi oliver, > > > > > > Thanks! Real space refinment was done in phenix with default > > settings. The position of these cysteines is quite constrained by > > where the main chain goes and the Phe you can see just next to the > > cysteine. To me it seems it would require very odd geometry to pull > > them into these centroids. > > > > > > All the best, > > > > Georg > > > > > > Von: Weiergräber, Oliver H. > > Gesendet: Mittwoch, 22. Dezember 2021 10:51:59 > > An: Hochberg, Georg; CCP4BB@JISCMAIL.AC.UK > > Betreff: RE: Strange cysteines > > > > Hmm, this may indeed be a disulfide bond, but the sulfur atoms do > > not seem to occupy their density centroids. > > They could be either _pushed_ apart by the refinement algorithm > > (which one are you using?) or _pulled_ apart due to incorrect > > geometry in their neighbourhood. > > > > Cheers > > Oliver > > > > == > > PD Dr. Oliver H. Weiergräber > > Institut für Biologische Informationsprozesse > > IBI-7: Strukturbiochemie > > Tel.: +49 2461 61-2028 > > Fax: +49 2461 61-9540 > > == > > > > > > > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of > > Hochberg, Georg [georg.hochb...@mpi-marburg.mpg.de] > > Sent: 22 December 2021 10:06 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: [ccp4bb] Strange cysteines > > > > Dear CCP4ers, > > > > > > We have recently solved the structure of an enzyme by cryoEM, which > > has two cysteines at its dimer interface, one in each monomer. The > > density around these two cysteines is very odd (see picture). They > > are too far apart for a disulphide bond, and there is nothing around > > these two cysteines that could help coordinate a metal. This density > > is also not a result of symmetry constraints in the density > > refinement either. We'd be very grateful for any ideas. > > > > [cid:b92417da-97f2-4dc3-9b5c-92278a5318fd] > > > > > > All the best and happy holidays, > > > > Georg Hochberg > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > > > > > > > Forschungszentrum Juelich GmbH > > 52425 Juelich > > Sitz der Gesellschaft: Juelich > > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > > Vorsitzender des Aufsichtsrats: MinDir Volker Rieke > > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > > Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, > > Prof. Dr. Frauke Melchior > > > > > > > > > > > > > > > > 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/ > 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
Re: [ccp4bb] AW: Strange cysteines
As you say, the Cys are too far apart for it to be a disulphide and it looks like oxidation of the Cys. This could be due to radiation damage, but other causes are possible. A former colleague had one in betaB1-crystallin, which is visible in pdbcode 1OKI at position 38. The difference density was quite clear before it was modeled as Cysteine sulfinic acid (CSD). Of course, it was easy to see at 1.4 Angstrom resolution. Andy Quoting "Hochberg, Georg" : Hi oliver, Thanks! Real space refinment was done in phenix with default settings. The position of these cysteines is quite constrained by where the main chain goes and the Phe you can see just next to the cysteine. To me it seems it would require very odd geometry to pull them into these centroids. All the best, Georg Von: Weiergräber, Oliver H. Gesendet: Mittwoch, 22. Dezember 2021 10:51:59 An: Hochberg, Georg; CCP4BB@JISCMAIL.AC.UK Betreff: RE: Strange cysteines Hmm, this may indeed be a disulfide bond, but the sulfur atoms do not seem to occupy their density centroids. They could be either _pushed_ apart by the refinement algorithm (which one are you using?) or _pulled_ apart due to incorrect geometry in their neighbourhood. Cheers Oliver == PD Dr. Oliver H. Weiergräber Institut für Biologische Informationsprozesse IBI-7: Strukturbiochemie Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 == From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Hochberg, Georg [georg.hochb...@mpi-marburg.mpg.de] Sent: 22 December 2021 10:06 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange cysteines Dear CCP4ers, We have recently solved the structure of an enzyme by cryoEM, which has two cysteines at its dimer interface, one in each monomer. The density around these two cysteines is very odd (see picture). They are too far apart for a disulphide bond, and there is nothing around these two cysteines that could help coordinate a metal. This density is also not a result of symmetry constraints in the density refinement either. We'd be very grateful for any ideas. [cid:b92417da-97f2-4dc3-9b5c-92278a5318fd] All the best and happy holidays, Georg Hochberg To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior 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/
[ccp4bb] AW: Strange cysteines
Hi oliver, Thanks! Real space refinment was done in phenix with default settings. The position of these cysteines is quite constrained by where the main chain goes and the Phe you can see just next to the cysteine. To me it seems it would require very odd geometry to pull them into these centroids. All the best, Georg Von: Weiergräber, Oliver H. Gesendet: Mittwoch, 22. Dezember 2021 10:51:59 An: Hochberg, Georg; CCP4BB@JISCMAIL.AC.UK Betreff: RE: Strange cysteines Hmm, this may indeed be a disulfide bond, but the sulfur atoms do not seem to occupy their density centroids. They could be either _pushed_ apart by the refinement algorithm (which one are you using?) or _pulled_ apart due to incorrect geometry in their neighbourhood. Cheers Oliver == PD Dr. Oliver H. Weiergräber Institut für Biologische Informationsprozesse IBI-7: Strukturbiochemie Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 == From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Hochberg, Georg [georg.hochb...@mpi-marburg.mpg.de] Sent: 22 December 2021 10:06 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange cysteines Dear CCP4ers, We have recently solved the structure of an enzyme by cryoEM, which has two cysteines at its dimer interface, one in each monomer. The density around these two cysteines is very odd (see picture). They are too far apart for a disulphide bond, and there is nothing around these two cysteines that could help coordinate a metal. This density is also not a result of symmetry constraints in the density refinement either. We'd be very grateful for any ideas. [cid:b92417da-97f2-4dc3-9b5c-92278a5318fd] All the best and happy holidays, Georg Hochberg To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior 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/
