I wonder if the high B factor, - 4 times higher you mentioned, is consistent with a sulfinic/sulfenic acid in rotation-so that the atoms dont appear resolved. -The two molecules are definitely in different environments so that even a small difference structure (or dynamics) there or access to oxygen could lead to only the one reacting under those conditions. We have seen similar things. This also could be consistent with -as you said, several data sets having this peak -if the crystals came from the same plates/vials for example, while another data set did not have the same oxidation condition and so did not. Can you refine the total occupancy of the peak, - perhaps using difference maps to see how much mass you need to account for there. That could give a clue Robert Stroud str...@msg.ucsf.edu
> On Aug 10, 2022, at 8:37 AM, Thomas, Leonard M. <lmtho...@ou.edu> wrote: > > This Message Is From an External Sender > This message came from outside your organization. > Thought of this originally but the peak is almost on top of the Sulfur and > with the oddly high B value I don’t think it is that. I would also think it > would show up on both monomers vs just one. > > Len > > >> On Aug 10, 2022, at 10:26 AM, Roger Rowlett <rrowl...@colgate.edu >> <mailto:rrowl...@colgate.edu>> wrote: >> >> Do you mean the sulfur atom density is larger, or do you mean there is a >> density peak adjacent to the sulfur atom? It is possible for cysteine (CYS) >> residues to be oxidized to S-hydroxycysteine (CSO) under certain storage or >> crystallization conditions. Ran into this in a cysteine hydrolase structure. >> >> Roger Rowlett >> Gordon & Dorothy Kljne Professor, Emeritus >> Department of Chemistry >> Colgate University >> >> On Wed, Aug 10, 2022, 11:00 AM Thomas, Leonard M. <lmtho...@ou.edu >> <mailto:lmtho...@ou.edu>> wrote: >> Hello All, >> >> I have run into something odd. In working on a structure for one of the >> groups I work with regularly, on one of the cystine residues I have a very >> large positive density peak at the sulfur position. The B value is >> approximately 4 times the other values in the residue and on other cystine >> residues. The overall structure has 2 molecules in the asymmetric unit and >> the corresponding cystine on the other monomer is behaving as I would >> expect. There are no disulfides in the structure. >> >> The data were collected on 9-2 at SSRL and all three of the data sets we >> collected show the same thing, all data go to about 2.2 angstroms. We are >> trying to determine the ligand binding in the molecule but this cystine is >> not involved in ligand binding. In house and other synchrotron data from >> previous protein preps and data collection runs of the same molecule grown >> in very similar condition and crystallized in the same space group have the >> residue behaving normally. >> >> I am open to any ideas as to what may be going on as I am rather puzzled by >> this. >> >> Thanks for any input, >> Len Thomas >> >> Leonard Thomas, Ph.D. >> Biomolecular Structure Core, Director >> Oklahoma COBRE in Structural Biology >> Price Family Foundation Institute of Structural Biology >> University of Oklahoma >> Department of Chemistry and Biochemistry >> 101 Stephenson Parkway >> Norman, OK 73019-5251 >> Office: (405)325-1126 >> lmtho...@ou.edu <mailto:lmtho...@ou.edu> >> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl >> <https://urldefense.com/v3/__http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl__;!!LQC6Cpwp!pz-QyKQA_nYjjdVeakNObKxTuJ9CIz5-Zaj7RdRcxNWkHHGMPe8nN0GRcFjIVUL7KtO-vaQTKANpt23TrWg$> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!GNU8KkXDZlD12Q!_bs6JkUE8llwkVdro0PtKJ88oV8Ct0vEnb1rF_5r8_Upwj2wXEk9ixHjpUKQq1VuS1nc0bkhsROTwnGpbMQ$> > > 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__;!!LQC6Cpwp!pz-QyKQA_nYjjdVeakNObKxTuJ9CIz5-Zaj7RdRcxNWkHHGMPe8nN0GRcFjIVUL7KtO-vaQTKANptQLlZ50$> ######################################################################## 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/
