Hi Stephen,
I think that while the PDB may accept the new numbering that you provide with
your truncated structure (I'm not sure about that though), it'll be quite
annoying for somebody who'd like to compare your structure with that of the
untruncated one. Besides, from what I've seen and experienced myself, residue
numbering in entries usually adheres to the position in the sequence. Also,
many structures are missing segments in the N-termini and the number of the
first residue is usually the correct sequence number and not 1. Upon deposition
you'll be asked to provide the information about the missing piece and its
position in the sequence.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Stephen Cusack
[cus...@embl.fr]
Sent: Friday, May 25, 2012 6:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDB deposition of internally truncated protein
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?
thanks
Stephen Cusack
--
**********************************************************************
Dr. Stephen Cusack,
Head of Grenoble Outstation of EMBL
Group leader in structural biology of protein-RNA complexes and viral proteins
Joint appointment in EMBL Genome Biology Programme
Director of CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host Cell
Interactions (UVHCI)
**********************************************************************
Email: cus...@embl.fr
Website: http://www.embl.fr
Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123
Fax: (33) 4 76 20 7199
Postal address: EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP181, 38042
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