Browsing backwards through a dozen or so of the most recent UNK-containing structures, I haven't found a counter-example yet - apart from those where the UNK residues are a single contiguous stretch and given their own chain ID. So a recent problem? ________________________________ From: Philip D. Jeffrey <pjeff...@princeton.edu> Sent: 12 February 2021 19:56 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>; Tristan Croll <ti...@cam.ac.uk> Subject: Re: Bug in mmCIF handling of UNK residues?
Doesn't seem to be the case for all instances: that table isn't present in 5BV0 despite the N-terminal residues of Nyv1 being modeled as UNK in the Vps16:Vps33:Nyv1 complex due to a symmetry overlap. Nyv1, C165-179 are UNK with partial occupancy, which is the N-terminal part of the model for that chain, then there's a gap of 3 missing residues, and then there's polypeptide model which we've assigned to sequence, all in the same chain. Not sure if the missing table is something that turned up after the deposition date (June 2015), or if it's related to the missing residues between the UNK segment and the defined amino acids. Phil Jeffrey Princeton ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Tristan Croll <ti...@cam.ac.uk> Sent: Friday, February 12, 2021 1:03 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Bug in mmCIF handling of UNK residues? Hi all, If I open (as far as I can tell) the mmCIF for any structure in the wwPDB that contains both defined amino acids and UNK in the same chain, then the UNK section is treated as covalently bonded to the flanking sequence. This appears to be a bug in the mmCIF generation itself, not in the viewing software (ChimeraX, in this case): if I look in 7kzn as a random example, I see: loop_ _pdbx_validate_polymer_linkage.id _pdbx_validate_polymer_linkage.PDB_model_num _pdbx_validate_polymer_linkage.auth_atom_id_1 _pdbx_validate_polymer_linkage.auth_asym_id_1 _pdbx_validate_polymer_linkage.auth_comp_id_1 _pdbx_validate_polymer_linkage.auth_seq_id_1 _pdbx_validate_polymer_linkage.PDB_ins_code_1 _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.auth_atom_id_2 _pdbx_validate_polymer_linkage.auth_asym_id_2 _pdbx_validate_polymer_linkage.auth_comp_id_2 _pdbx_validate_polymer_linkage.auth_seq_id_2 _pdbx_validate_polymer_linkage.PDB_ins_code_2 _pdbx_validate_polymer_linkage.label_alt_id_2 _pdbx_validate_polymer_linkage.dist 1 1 C X UNK 345 ? ? N X UNK 348 ? ? 10.08 2 1 C X UNK 396 ? ? N X UNK 403 ? ? 28.65 3 1 C Y UNK 281 ? ? N Y UNK 284 ? ? 6.72 4 1 C Y UNK 387 ? ? N Y UNK 394 ? ? 22.26 5 1 C Y UNK 420 ? ? N Y UNK 424 ? ? 12.82 Considering that the coords themselves generally seem fine, I guess this is happening post deposition? Best regards, Tristan ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
