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 <a.purk...@mail.cryst.bbk.ac.uk> 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" <georg.hochb...@mpi-marburg.mpg.de>: > > > 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. <o.h.weiergrae...@fz-juelich.de> > > 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.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
