Another solution, which I recall using when I was processing data
at the PDB at BNL, is to make use of the insertion code field.
All the residues of the first portion could have A appended to
their residue number and all the residues of the second portion
could have B appended to their residue number.  The only problem
would occur if there was need for an insertion code in the original
numbering of each portion.

                                 Frances Bernstein

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On Tue, 16 Oct 2007, Stevens, James (CDC/CCID/NCIRD) wrote:

> Hi Sebastiano,
> Discuss things with the person who processes your deposition to the PDB.
> We did the same for an uncleaved influenza protein. Normally two chains
> but because it was uncleaved we provided a justification for numbering
> as two chains (pdb:1RD8). In order to make it consistent with the
> numbering for the existing structures, the pdb people were very obliging
> and agreed that things would be simpler for people to be able to compare
> with what was already out there. I used pdbset to change the numbering,
> added a link between the two virtual chains and together with the pdb
> people we put together a remark in the pdb header to describe what is
> going on. They were very helpful.
> Best wishes
> James
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Sebastiano Pasqualato
> Sent: Tuesday, October 16, 2007 6:33 AM
> To: [log in to unmask]
> Subject: [ccp4bb] chain IDs and residue numbering in depositing chimeras
> PDB
>
> Dear all,
> I'm going to deposit to the PDB a structure in which a polypetidic chain
> is made up by the fusion of two portions of proteins.
> That is, it is a chimera of two proteins (say aa 1-100 of protein X
> fused to aa 50-150 of protein Y) Currently, this polypetidic chain has
> got a single chain ID and I've kept residue numbers growing without
> caring about the original residue numbers of the second protein (i.e.
> the chain A goes from residue 1 to 100, then 101 to 201 correspond to
> residues 50-150 of protein Y)
>
> Now, I've always found it nice to have the correct numbering on the
> residues, when I download a pdb, and was wondering if any of you could
> suggest me a way to have this in my structure.
> I wouldn't like to change the chain ID, a) beacuse what's crystallized
> was a single polypeptidic chain b) because many programs will not put a
> link between residues with different chain IDs A solution would be
> adding something like "1000" to the numbers of the residues of the
> second protein, but then again the residues numbers will jump from 100
> to 1050 and there will be no link created by some programs (isn't
> it?)...
>
> How could I do? Any suggestion is warmly welcomed!
>
> Thanks in advance for the help,
> Sebastiano
>
>
> --
> Sebastiano Pasqualato, PhD
> IFOM-IEO Campus
> Dipartimento di Oncologia Sperimentale
> Istituto Europeo di Oncologia
> via Adamello, 16
> 20139 Milano
> Italy
> tel +39 02 9437 5094
> fax +39 02 574 303 310
>