Re: [phenixbb] Validation of structure with modified residue

Hi Xavier, I remember we had a similar case in January and had a long conversation about it between Nigel, Oleg and me. The solution at that time was to update Phenix library with that non-standard amino-acid-like entity so that Phenix produces mmcif file that is legible by PDB. In your case it does seem you have "SER plus something" as the modified residue. I think the easiest way for you to proceed is to follow Nigel's suggestion. Pavel On 4/20/22 14:10, Nigel Moriarty wrote:

Xavier

I'm sure others can solve this problem but it adds to my point that if you have a covalently bound ligand to an amino acid that does not change the main chain, it is generally "better" to maintain the, in this case SER, and generate the ligand and links to the side chain.

Just one of a number of reasons.

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 : [email protected] Fax   : 510-486-5909      Web  : CCI.LBL.gov http://CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 https://orcid.org/0000-0001-8857-9464

On Wed, Apr 20, 2022 at 2:02 PM Xavier Brazzolotto 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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