Dear Tony
The only requirements we have for numbering is that every residue must
be unique when using a combination of residue name (to handle
microheterogeneity), residue number, insertion code and chain ID.
During curation we will try to map your protein sequence to UniProt -
please see the following documentation on this process:
https://www.wwpdb.org/documentation/procedure#toc_1
The exact numbering scheme you choose is up to you (especially for
expression tags), however users of your entry may find it difficult to
use your entry is you decided to number your protein randomly or with
decreasing residue numbers. We may suggest that you changed the
numbering if you did this.
Our official wording from the above link is:
"The wwPDB encourages deposition of polymer chains with sequential
residue numbering. For protein chains, the authors are encouraged to
follow the UniProt residue numbering, wherever possible. The use of
non-sequential residue numbering and insertion codes should be avoided
as far as possible in order to make structures easily interpretable by
the larger scientific community. If the coordinate residue numbers, as
provided by the author, are unique and sequential within a particular
chain ID, the residues will not be renumbered."
this is from the section "How are chain IDs related to residue numbering?"
I hope this helps
John
PDBe
On 19/09/2017 13:51, herman.schreu...@sanofi.com wrote:
Hi Dave and Tony,
Upon submission, the pdb checks the sequence and automatically
generates comments about sequences derived from the expression vector.
So you do not have to do anything. Given the issues many programs have
with non-sequentially numbered residues, I would also number them 7,8,9.
Best,
Herman
*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
von *Briggs, David C
*Gesendet:* Dienstag, 19. September 2017 14:24
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* Re: [ccp4bb] question regarding sequence numbering
Hi Tony,
When I've had similar issues, I've numbered them sequentially (i.e.
7,8,9) and remarked in the PDB header that they are vector-derived
sequence.
I believe that is what the PDB ask you to do in situations like this
(maybe they can comment?).
If they are not numbered sequentially, then often graphics and
refinement software won't treat them as linked.
Dave
--
Dr David C Briggs
Hohenester Lab
Department of Life Sciences
Imperial College London
UK
http://about.me/david_briggs
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From: Antonio Ariza
Sent: Tuesday 19 September, 13:15
Subject: [ccp4bb] question regarding sequence numbering
To: ccp4bb@jiscmail.ac.uk <mailto:ccp4bb@jiscmail.ac.uk>
Hi all,
Here's a problem I haven't come across before. I'm working on a
structure whose expression plasmid was designed to remove the first 9
amino acids from the protein of interest and to which an N-terminal
tag was added. After cleaving the tag I am left with 3 amino
acids (GPM) followed by the original sequence. Obviously the residues
of interest should follow the numbering of the original sequence (i.e.
10, 11, 12, ...). What numbers would you assign to the first 3
residues (GPM)? 7, 8, 9? -2, -1, 0?
Cheers,
Tony
------------------------------------------------------
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