Dear all, I have a couple of questions regarding deposition of a structure with a posttranslational modification.
1. I understand, that PCMs (protein chemical modifications) and PTMs are now handled in a standard way, but what is the standard way? Is there a link giving insight into these rules? 2. Specifically, I have a cacodylate (dimethylarsenic acid) modified serine. A very similar modification, phosphoserine, has its own three letter code, SEP. The cacodylate modification is handled as serine and cacodylate (CAC) with a link record (in entry 1LZK). What is the correct handling? 3. For SER-CAC I could not find an existing link.cif file for refinement. I rather created a DRG.cif file for the modified serine and used this for refmac and coot. This works, but how should I deposit this? The modified residue would clash with the existing combination of SER / CAC / SER-CAC link. 4. Can I exchange the modified serine by a serine plus cacodylate in the cif file without going through refmac (I don't have the link.cif file)? In pdb format I would simply exchange the ATOM lines, but in cif format? 5. Once I have a cif file with separate SER and CAC residues, I have to reupload the renamed coordinates again in the deposition process, thereby loosing all extra information I typed in already. Can I prevent this loss? (ok, that's a minor problem) Best rergards Gottfried Dr. Gottfried Palm Universität Greifswald Inst. für Biochemie (MNF) Synthetische und Strukturelle Biochemie Felix-Hausdorff-Straße 4 17489 Greifswald ######################################################################## 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/
