[phenixbb] Coot mutation of Asp residue to isoAsp residue

Xiao Lei xiaoleiusc at gmail.com
Tue Aug 18 10:56:11 PDT 2015

Hi Zhejie,

For the 1AT6 structure, I downloaded its density in coot using "fetch
density from EDS", but when I found the IAS at 101 position and try to do
real space refine, it gives an error that "Refinement setup failure. Failed
to find restraints for IAS."

I do not know how to fix this but it seems to me it's caused by incomplete
restraints dictionary or monomer library in ccp4?



On Tue, Aug 18, 2015 at 10:42 AM, Xiao Lei <xiaoleiusc at gmail.com> wrote:

> Hi Zhijie,
> Thank you very much for the information. For step 1 you mentioned, I can
> get monomer with L-Asp but it seems I can not drag it (or I do not know how
> to do) and can not delete or modify it to become isoAsp. I will try play
> around more though.
> Xiao
> On Mon, Aug 17, 2015 at 6:33 PM, Zhijie Li <zhijie.li at utoronto.ca> wrote:
>> Hi Xiao,
>> IsoAsp is essentially an L-Asp linked with next aa through its side chain
>> (beta) carboxyl. So the mutation button won’t help you. You need to build
>> in a new L-ASP, which is treated as a covalently linked ligand (HETATM
>> records), instead of a standard residue (ATOM records) of the protein chain.
>> A practical method might be: 1) delete the original Asp, 2) import a free
>> L-Asp using “get monomer”, delete its hydrogen atoms and drag it into the
>> density, delete one oxygen atom on the beta-carboxyl and change the
>> residue’s numbering and chain id to fit it into the sequence,  3) edit the
>> PDB, if necessary, to turn the ASP into a ligand (a HETATM record inside
>> the chain).
>> For step 3, you may need to rename the ASP to something else (IAS was
>> used for isoASP in older pdb, so I would go with IAS ) so that coot won’t
>> try to make a regular peptide bond using its main chain carboxyl during
>> real space refinement. Of course you will need to make a cif file for the
>> “new” compound too. I guess you can make a copy of ASP.cif from the monomer
>> library and change everything in it to IAS. I think if you have placed the
>> IAS to the right location and its ends are in bonding distance with the
>> neighbouring aa residues you may not need to do anything for refmac. For
>> phenix.refine you will need to add a bond description to the .edit file for
>> each linkage the IAS makes to the neighboring aas.
>> You may take a look at the structure 1AT6 and its PDB file. The residue
>> IAS 101 is an example of isoASP. Note that the IAS atoms are HETATM in the
>> chain and there are two LINK records in the header to indicate its linkage
>> to neighbouring aas (LINK records are normally not generated or needed
>> during refinement using refmac or phenix.refine).
>> Zhijie
>> *From:* Xiao Lei <xiaoleiusc at gmail.com>
>> *Sent:* Monday, August 17, 2015 6:50 PM
>> *To:* PHENIX user mailing list <phenixbb at phenix-online.org>
>> *Subject:* [phenixbb] Coot mutation of Asp residue to isoAsp residue
>> Dear Phenixbb members,
>> I suspect one Asp residue in my model may be an isoAsp (isomerization of
>> Asp). I am asking if there is way to mutate Asp residue to
>> isoAsp(isoaspartic acid) residue in coot GUI (I'm using coot 0.8.1 EL in
>> Mac OS X10.10.5)?
>> I know there is a mutation button on coot, but the mutated aa lists are
>> all natural amino acids. If I have to delete the Asp residue first and then
>> build isoAsp into the density map, is there a way in coot to build an
>> isoAsp residue in map?
>> Thanks ahead.
>> Xiao
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