Re: [ccp4bb] AW: [ccp4bb] question regarding sequence numbering

2017-09-20 Thread John Berrisford 

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 





From: Antonio Ariza

Sent: Tuesday 19 September, 13:15

Subject: [ccp4bb] question regarding sequence numbering

To: 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

--

*Dr. Antonio Ariza*

*University of Oxford*

*Sir William Dunn School of Pathology*

*South Parks Road*

*Oxford*

*OX1 3RE*

*e-mail: *antonio.ar...@path.ox.ac.uk 

*Tel: 00 +44 1865 285655*

*Links to my public profiles:*

ResearchGate 



LinkedIn 



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[ccp4bb] AW: [ccp4bb] question regarding sequence numbering

2017-09-19 Thread Herman . Schreuder 
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


From: Antonio Ariza
Sent: Tuesday 19 September, 13:15
Subject: [ccp4bb] question regarding sequence numbering
To: 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
--
Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE
e-mail: antonio.ar...@path.ox.ac.uk
Tel: 00 +44 1865 285655

Links to my public profiles:
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LinkedIn
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Twitter

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