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: [email protected] 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: [email protected]<mailto:[email protected]> Tel: 00 +44 1865 285655 Links to my public profiles: ResearchGate<https://www.researchgate.net/profile/Antonio_Ariza> LinkedIn<https://www.linkedin.com/in/antonioariza1> GoogleScholar<https://scholar.google.co.uk/citations?user=9pAIKV0AAAAJ&hl=en> Twitter<https://twitter.com/DrAntonioAriza?lang=en> Check out my latest paper!!! Structural insights into the function of <http://www.nature.com/articles/ncomms15847> ZRANB3<http://www.nature.com/articles/ncomms15847> in replication stress response<http://www.nature.com/articles/ncomms15847>
