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<https://urldefense.proofpoint.com/v2/url?u=http-3A__about.me_david-5Fbriggs&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=eXDpcWadyxbrjW5lOO-Vg-tud-0wh7P_EIdo3UxkBjU&s=CuEDTUtv1fMER1EIW76hQoC60eF1_StruW8oW9VKyFY&e=> From: Antonio Ariza Sent: Tuesday 19 September, 13:15 Subject: [ccp4bb] question regarding sequence numbering To: ccp4bb@jiscmail.ac.uk<mailto: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<mailto:antonio.ar...@path.ox.ac.uk> Tel: 00 +44 1865 285655 Links to my public profiles: ResearchGate<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Antonio-5FAriza&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=eXDpcWadyxbrjW5lOO-Vg-tud-0wh7P_EIdo3UxkBjU&s=JlLk_YBvsa_Pqy9U6uSWCiAB3dyF_ZQR0H_nXk4grZE&e=> LinkedIn<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_antonioariza1&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=eXDpcWadyxbrjW5lOO-Vg-tud-0wh7P_EIdo3UxkBjU&s=DbSwK3yLqHH92Pr-7NaQyVmzSSScEZ3jt8rNCa9zMbQ&e=> GoogleScholar<https://urldefense.proofpoint.com/v2/url?u=https-3A__scholar.google.co.uk_citations-3Fuser-3D9pAIKV0AAAAJ-26hl-3Den&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=eXDpcWadyxbrjW5lOO-Vg-tud-0wh7P_EIdo3UxkBjU&s=MmllbCLL0qpk3UuRY8tL6a3rtsHzxmeIXQ5QM7i4rlo&e=> Twitter<https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_DrAntonioAriza-3Flang-3Den&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=eXDpcWadyxbrjW5lOO-Vg-tud-0wh7P_EIdo3UxkBjU&s=Y-LOBkfQFCKxgiUgTRzNEZXrPFeOzJpt2OOBVMfaQ4Q&e=> Check out my latest paper!!! Structural insights into the function of <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nature.com_articles_ncomms15847&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=eXDpcWadyxbrjW5lOO-Vg-tud-0wh7P_EIdo3UxkBjU&s=ajttqwr7ED8_WBG6ALc86GNNTa7qa_WbddCP5AHlUd4&e=> ZRANB3<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nature.com_articles_ncomms15847&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=eXDpcWadyxbrjW5lOO-Vg-tud-0wh7P_EIdo3UxkBjU&s=ajttqwr7ED8_WBG6ALc86GNNTa7qa_WbddCP5AHlUd4&e=> in replication stress response<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nature.com_articles_ncomms15847&d=DwMFAg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=eXDpcWadyxbrjW5lOO-Vg-tud-0wh7P_EIdo3UxkBjU&s=ajttqwr7ED8_WBG6ALc86GNNTa7qa_WbddCP5AHlUd4&e=>
