[phenixbb] Validation of structure with modified residue

Thu Apr 21 09:29:30 PDT 2022

Xavier

I'm happy to take a closer look. Send me the two entities (SER and ligand)
along with the restraints and I will try to help.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909      Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464

On Thu, Apr 21, 2022 at 8:32 AM Xavier Brazzolotto <xbrazzolotto at gmail.com>
wrote:

> I recall now how I used to add the glycans before the Carbohydrate Module
> in Coot.
> I have to make the cif file with the putative O atom of SER OG and remove
> it before making the bond.
> I will try that, it will certainly correct my geometry issue but I am
> still not sure for the final file and validation.
>
> Fingers crossed...
>
> Le 21 avr. 2022 à 17:09, Xavier Brazzolotto <xbrazzolotto at gmail.com> a
> écrit :
>
> After some careful inspection.
> The geometry on the C atom of the ligand is weird, I don’t get something
> close to tetrahedral (or similar).
> Probably some angles are missing or I did something wrong with the ligand
> cif file.
> Not fixed yet
>
> Le 21 avr. 2022 à 13:39, Xavier Brazzolotto <xbrazzolotto at gmail.com> a
> écrit :
>
> I’ve re-processed the structure separating the SER residue from the ligand
> part. Now I have independent ligand.
> In the « Custom Geometry Restraints »  I’ve defined the bond between OG
> and the carbon atom of the ligand and I’ve defined the angles (I’ve used
> the values from the previously determined eLBOW run off the SER-bound
> ligand complex), saved the restraints and launched the refinement. At a
> first look it was processed correctly and the final cif file has now the
> whole protein in Chain A.
>
> I’ve used prepare PDB deposition using the FASTA sequence of the protein
> (wonder if I have to provide the ligand CIF file and add more options) and
> ran phenix.get_pdb_validation : the report looks ok for protein and some
> other basic ligands (sugars, buffer, glycerol, etc...) but the ligand of
> interest was not processed (EDS FAILED...). In the PDB file, all these
> extra ligands are also in Chain A, with water in chain B.
>
> If I try the validation through the website (PDBe at EBI) with both cif
> files from the Refine or the Prepare_PDB_Deposition process, both seem to
> crash the server as it takes forever without Finalizing...
>
> I wonder if I am missing something… Maybe declaration of removal of atoms
> : HG bound to OG in SER or/and removal of one H from the carbon of the
> ligand involved in the bond ?
>
> Xavier
>
> Le 21 avr. 2022 à 08:06, Xavier Brazzolotto <xbrazzolotto at gmail.com> a
> écrit :
>
> Thank you for your feedback.
>
> @Paul, I’ve run the « Prepare model for deposition » with the option
> modified residue (SLG). Not sure it will change if I change the name as it
> is already the PDB database, but I will give it another try.
>
> I think that I will have to describe only the ligand and add some
> parameters restricting distance and angles between the OG of SER and the
> ligand, I think this is right way.
> @ Nigel, is that what you mean with « details » ? If you have any other «
> tips/tricks » they are welcome.
>
> Best
> Xavier
>
> Le 21 avr. 2022 à 02:47, Nigel Moriarty <nwmoriarty at lbl.gov> a écrit :
>
> Xavier
>
> Paul's point is very valid because the "Prepare for Deposition" step is
> what generates the sequence (which is the crucial point here) for
> deposition. However, because you have "created" a new amino acid, there
> will still be issues as highlighted by Pavel. It is a corner case.
>
> One small addition point is that SLG is already taken in the PDB Ligand
> list. There are tools in Phenix to find an used code.
>
> Can you re-engineer it with SER+ligand? This will solve the problem using
> the current Phenix version. I can help with the details if needed.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov <NWMoriarty at LBL.gov>
> Fax   : 510-486-5909      Web  : CCI.LBL.gov <http://cci.lbl.gov/>
> ORCID : orcid.org/0000-0001-8857-9464
>
>
> On Wed, Apr 20, 2022 at 5:02 PM Paul Adams <pdadams at lbl.gov> wrote:
>
>>
>> Please also remember that you need to run “Prepare model for PDB
>> deposition” (in the GUI under "PDB Deposition") on the mmCIF file you get
>> from phenix.refine. This provides important information that is required
>> for the deposition at the PDB.
>>
>> On Apr 20, 2022, at 1:58 PM, Xavier Brazzolotto <xbrazzolotto at gmail.com>
>> wrote:
>>
>> Dear Phenix users,
>>
>> I don’t know if my problem is related to Phenix but for information I’m
>> running Phenix 1.20.1-4487 under MacOS 12.3.1.
>>
>> I’ve finalized a structure where a ligand covalently modified the protein.
>>
>> I’ve generated the modified residue (named SLG for serine modified by
>> ligand). For this I’ve generated the molecules in SMILES and used eLBOW to
>> generate the restraints. Then I’ve modified the cif file defining the
>> molecule as a L-peptide and replacing the atom names of the Serine part
>> (CA, CB, OG, C, O, N, and OXT)
>> In coot (from CCP4 : 0.9.6 EL), I’ve used the modified cif file and it
>> allowed merging of the modified residue into the polypeptide chain as
>> expected and further refinements went without any issue in Phenix
>> (providing the modified cif file of course). Everything seems well
>> interpreted. So far so good.
>>
>> However, now I would like to validate the structure and both Phenix
>> validation tool and the PDB web server do not accept the final cif file.
>>
>> Checking this file I’ve noticed that the protein seems split into 3
>> pieces (chain A, first residue up to the one before the modified residue;
>> chain B the modified residue by itself described as HETATM and chain C the
>> rest of the polypeptide up to the C-ter).
>> The PDB file presents only one chain A for the whole protein with the
>> modified residue...
>>
>> I don’t know if this is an issue with Phenix generating this final cif
>> file in this specific case or if I need to modify this final file by hand ?
>>
>> Any help is welcome.
>> Thanks
>>
>> Xavier
>>
>>
>>
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>> --
>> Paul Adams (he/him/his)
>> Associate Laboratory Director for Biosciences, LBL (
>> https://biosciences.lbl.gov/leadership/)
>> Principal Investigator, Computational Crystallography Initiative, LBL (
>> https://cci.lbl.gov)
>> Vice President for Technology, the Joint BioEnergy Institute (
>> http://www.jbei.org)
>> Principal Investigator, ALS-ENABLE, Advanced Light Source (
>> https://als-enable.lbl.gov)
>> Division Deputy for Biosciences, Advanced Light Source (
>> https://als.lbl.gov)
>> Laboratory Research Manager, ENIGMA Science Focus Area (
>> http://enigma.lbl.gov)
>> Adjunct Professor, Department of Bioengineering, UC Berkeley (
>> http://bioeng.berkeley.edu)
>> Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (
>> http://compbiochem.berkeley.edu)
>>
>> Building 33, Room 250
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>> Tel: 1-510-486-4225
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>> ORCID: 0000-0001-9333-8219
>>
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>>
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