Maybe a crazy idea, but couldn't one use various model/geometry validation tools to figure out some of those ambiguities? As a test one could take a very good 1.7A structure and do some random ASN->ASP, THR->VAL etc mutations followed by refinement (including hydrogens). Wouldn't some validation tool pick up unfavourable conformations, poor rotamers and/or hydrogen clashes and poor H-networks (compared to the initial, correct sequence)?
Maybe there is some kind of "fingerprint" in validation results for such incorrect residue assignments that can distinguish correct from incorrect sequences ... Or put another way, if model validation can not pick up such sequence errors: should we be worried about the reliability of our validation criteria? A large scale re-refinement of deposited structures with (1) the current/correct sequence and (2) those ASN/ASP, THR/VAL etc ambiguities artificially introduced, could provide a clever algorithm (AI?) with the data basis to figure out those "fingerprints". Maybe even for the ASN/GLN/HIS side-chain orientations when the sequence is actually correct. Cheers Clemens On Fri, Jul 29, 2022 at 12:08:58PM +0000, Jon Cooper wrote: > Thank you so much for your replies. I apologise for being unclear. The > protein is purified from a plant that hasn't had its genome sequence > determined. We know the enzyme family of the protein and therefore the > structure was originally solved by MR. The 'X-ray sequence' we have is just > determined from looking at the 1.7 Angstrom density, which is good, over > several refinement and rebuilding rounds. The resulting sequence has been run > through blast and it is up to 58% identical with other family members. To me > this seemed low but that degree of identity is typical of other family > members. The postgrad who did the work did obtain some peptide sequences and > prior to that about 20% of the sequence was determined by the Edman method > with the usual Asp/Asn and Glu/Gln ambiguity. However, there isn't any > prospect of us doing further experimental work, sorry, but that's the way it > is!! > > Best wishes, Jon.C. > > Sent from ProtonMail mobile > > -------- Original Message -------- > On 29 Jul 2022, 12:23, Jan Dohnalek wrote: > > > If you know at least something about your protein, organism, type of > > molecule, ..., you could try mass spectrometry peptide mapping to known > > sequences, this may give you some answers for the ambiguities you might be > > seeing, if nothing else .. > > > > Jan > > > > On Fri, Jul 29, 2022 at 12:15 PM Jon Cooper > > <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > > > >> Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray > >> sequence for a protein where it is impractical to do experimental > >> sequencing, protein or DNA. The structure refines to publishable R/R-free > >> and the main ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where > >> alternative H-bonding networks are possible. Running alpha-fold seems an > >> interesting option? Any suggestions much appreciated. > >> > >> Cheers, Jon.C. > >> > >> Sent from ProtonMail mobile > >> > >> --------------------------------------------------------------- > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > -- > > > > Jan Dohnalek, Ph.D > > Institute of Biotechnology > > > > Academy of Sciences of the Czech Republic > > Biocev > > Prumyslova 595 > > 252 50 Vestec near Prague > > Czech Republic > > Tel. +420 325 873 758 > > ######################################################################## > > 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/ -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *-------------------------------------------------------------- ######################################################################## 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/
