Dear Stephen, On Fri, 2012-05-25 at 17:42 +0200, Stephen Cusack wrote: > Dear All, > I need to deposit in the PDB the co-ordinates of a protein with an > internal truncation. > If I do this in the normal way with consecutive numbering according to > the actual polypeptide sequence > in the crystal, the residue numbers after the truncation will not > correspond to the equivalent residues > in the untruncated protein (of which there is also a structure). Is > there any good solution to this problem?
I'm a little out of touch with this now, but AFAIK you should be able to number the residues according to whatever scheme you like. There is nothing new about keeping consistent residue numbers across multiple structures that have insertions and/or deletions - antibodies are the classic case. As long as you give the truncated sequence in your deposition rather than the untruncated one (so that it reflects what you actually crystallised rather than the canonical or wild-type sequence), the PDB should be fine with your chosen residue numbering scheme. You may need to provide information about the conflicts between the truncated sequence and the canonical one found in UniProt if your particular sequence doesn't correspond to one of the variants already known to UniProt. If you don't already know the UniProt accession code for your protein, you may find that it helps the deposition process if you find the correct one before deposition rather than leaving it up to the PDB to look for it. Good luck, and kudos for thinking about this before depositing! Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
