Thank you very much for all the helpful replies. I have summarised the
discussion here:
https://justpaste.it/9cfl9
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent with [Proton Mail](https://proton.me/) secure email.
Sent: Friday, July 29, 2022 9:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Checking X-ray sequence (no more protein).
Hi Jon,
There are placeholders for ASP/ASN and GLU/GLN ambiguities: ASX and GLX
respectively. You can just use those. AFAICT there no such thing for VAL/THR
Hi Jon,
There are placeholders for ASP/ASN and GLU/GLN ambiguities: ASX and GLX
respectively. You can just use those. AFAICT there no such thing for VAL/THR
ambiguities. You could look for the most likely canadidata based on multiple
sequence alignments. Refinement of both alternatives can
Thank you, yes, threading style tools to assess the likelihood of having a
given amino acid in a certain position in the fold would be a good approach. I
have tried one but wasn't hugely informative, in my hands anyway. All
suggestions very welcome but big database science is a bit outside my
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
Dear Jon,
We did exactly the same back in 1999's.
1) Natesh R, Bhanumoorthy P, Vithayathil PJ, Sekar K, Ramakumar S,
Viswamitra MA. (1999). Crystal structure at 1.8 Å resolution and proposed
amino acid sequence of a thermostable xylanase from *Thermoascus
aurantiacus*. J. Mol. Biol., 288,
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
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 <
