Missing residues in PDB file
Hello,
I would like to perform a research on 4za7 protein. As long as using Modeller to insert missing residues is rather straightforward, the issue I have encountered is more related to PDB file itself. In the remark 465 section in the original pdb file, there are listed several missing residues:
REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 ASN A 499A REMARK 465 LEU A 499B REMARK 465 GLU A 499C REMARK 465 HIS A 506 REMARK 465 HIS A 507
The problem is that I lack the knowledge on how to deal with those residues: 499A, 499B, 499C. I would most likely just insert 499A into the structure that will be further analysed but in regular residues that are normally placed in pdb file there is already a residue numbered 499. For some reason though, there are no residues 500 and 501 in the pdb file.
How should I proceed with it? Should I just ignore those different options for residue number 499 and go with the one that was properly determined by X-ray experiment, or should I do something else? Any suggestions from more experienced researchers will be welcome.
Kind regards, Szymon Zaczek
On 07/11/2017 02:26 AM, Szymon Żaczek wrote: > I would like to perform a research on 4za7 protein. As long as using > Modeller to insert missing residues is rather straightforward, the > issue I have encountered is more related to PDB file itself. In the > remark 465 section in the original pdb file, there are listed several > missing residues: ... > The problem is that I lack the knowledge on how to deal with those > residues: 499A, 499B, 499C.
What's the complication? Modeller doesn't care how the PDB residues are numbered - just treat these in exactly the same way as any other missing residue. The output model is always numbered sequentially starting at 1.
Ben Webb, Modeller Caretaker
On Tue, Jul 11, 2017 at 11:26 AM, Szymon Żaczek szymonzaczek@gmail.com wrote:
> The problem is that I lack the knowledge on how to deal with those > residues: 499A, 499B, 499C. I would most likely just insert 499A into > the structure that will be further analysed but in regular residues > that are normally placed in pdb file there is already a residue > numbered 499. For some reason though, there are no residues 500 and > 501 in the pdb file.
The numbering in the PDB files is messy. In order to preserve the numbering with the literature (so if residue 700 is interesting, all the papers will use the same number), they may skip some numbers or add variations (like 499A). You may also need to mutate the structure in order to crystallise it, or you won't see some other residues.
Your best bet to complete it is to align the sequence provided by the PDB ( http://www.rcsb.org/pdb/download/viewFastaFiles.do?structureIdList=4ZA7&...) to the sequence extracted from the structure, see if you have gaps, and model them.
/David.
participants (3)
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David Menéndez Hurtado -
Modeller Caretaker -
Szymon Żaczek