Dear Michelle, CSO is a peptide in the latest monomer library, which is included in CCP4 9.0. I suppose you are using an old version. At least the first issue may be sorted by using COOT from CCP4 9.0.
Best regards, Keitaro On Tue, 8 Oct 2024 at 13:30, Michelle Miller <[email protected]> wrote: > > Hi, > > > > I’m trying to model a N-O-S bond between a lysine side-chain and an oxidised > cysteine (CSO) as described in > https://www.nature.com/articles/s41467-024-48109-3 > > > > I’m facing two problems in Coot (v 0.9.8.3): > > > > Firstly, when I go >Replace residue and replace the cysteine with a CSO – > Coot does not recognise the CSO as part of the peptide chain. I can manually > (roughly) put it in place and Phenix will fix it during refinement, however > this continues to be a problem for coot. > > > > Secondly, I have tried a couple of ways to model the NOS bond and none of > them seem to work correctly. > > > > I defined the link using JLigand, saved the cif file and the LINK record. I > manually put this link in place in Coot, loaded the cif file into Phenix and > it sort of worked, although the O-N bond length is too long and doesn’t match > what is defined in the cif file (~1.99 Å vs 1.38 Å). Furthermore, after > loading the cif file in coot, when I try to do a real space refine, it does > not recognise the O-N link (or the CSO as part of the peptide chain as > described above). > I defined the entire CSO-LYS as a ligand and generated cif restraints in > Phenix using elBOW, loaded the pdb into Coot and placed into the density, > merged with the pdb and tried to define “links” to the peptide backbone on > both sides. As above, these bonds are not recognised by coot. After running > through phenix, the planarity of the amide bonds is lost. > > > > To add to the complexity, there are two conformations of the N-O-S > modification/linkage, so I also want to be able to model that. > > > > Any help would be greatly appreciated!! > > > > Thanks, > > Michelle > > > > --------------------------------------- > > Michelle Miller PhD > > Senior Research Officer > > Structural Biology > > > > E [email protected] > > > > > Walter and Eliza Hall Institute of Medical Research > 1G Royal Parade Parkville Victoria 3052 Australia > > www.wehi.edu.au > > Twitter | Facebook | Instagram | Youtube | LinkedIn > > > > WEHI acknowledges the Wurundjeri people of the Kulin Nation as the > traditional owners of the land where our campuses are located and the > continuing connection to country and community. > > Private and confidential > The content of this e-mail and any attachments may be private and > confidential, intended only for use of the individual or entity named. If you > are not the intended recipient of this message you must not read, forward, > print, copy, disclose, use or store in any way the information this e-mail or > any attachment contains. If you are not the intended recipient, please notify > the sender immediately and delete or destroy all copies of this e-mail and > any attachment. > > > ________________________________ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
