Dear Phil and Jared, Thank you very much for your kind and detailed advice; it helped me resolve this issue. I appreciate it! Best, Lan
On Apr 30, 2025, at 1:49 PM, Phil Jeffrey <[email protected]> wrote: CAUTION: This email originated from outside of TTUHSC. Do not click links or open attachments unless you recognize the sender and know the content is safe. Dear Lan, You can give the His-tag residues the same number as the previous residue, combined with insertion codes (A-Z). e.g. XXX20 - HIS20A - HIS20B - ... - HIS20F - YYY21 This is similar to what is done with insertions in e.g. antibody CDR H3 loops. You can refer to the PDB specification for more info, e.g. column 27 ("iCode") here: https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM<https://urldefense.com/v3/__https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html*ATOM__;Iw!!PZU9J6Y!YeKllVErDxzKOJIP6y6-4EBoGvQDrkJIrfDSfx7fwOqj2lLCUuuKgfPM-jptBEsl8l5K_TJ3ECaZXqzwAJ3FzfAkQvc_Sg$> I tend to edit insertion codes and residue numbers for the specific inserted residues manually (e.g. in Vim), then use e.g. Coot or another program (e.g. pdbset) to renumber the following residues. Maybe others can chime in with other tools that might be useful. Cheers, Jared Hello Lan In PDB format your option would be insertion codes, column 27 (counting starting at character 1, not 0), right after the residue number. If, for example, you had a hexa-HIS after residue 22 you could call them 22A, 22B, 22C, 22D, 22E, 22F before resuming with the native protein sequence at residue 23. https://urldefense.com/v3/__http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_62.html__;!!PZU9J6Y!YawdpyB00KLGNymwnrVuXHMmxuZJXNZ5PFfr8IvflgM0wRUnWdK4OyOpZ__2xOwHisfLdoFCnmaznxbmQuj2CUiU$ Phil On 4/30/25 2:24 PM, Guan, Lan wrote: Dear All, I am working on a protein structure with a His tag in the middle of the protein. I would appreciate advice on retaining the native number in the protein sequence after this His tag. Best, Lan *********************************************************************************** Lan Guan, MD, PhD Professor | Department of Cell Physiology and Molecular Biophysics Co-Director | Center for Membrane Protein Research 3601 4th St. MS 6551 Texas Tech University Health Sciences Center Lubbock, TX 79430 5A148A (Office)| (1) 806 743-3102 (Phone) | [email protected] (E-Mail) https://www.ttuhsc.edu/medicine/cell-physiology-molecular-biophysics/faculty/guan/ https://www.ttuhsc.edu/centers-institutes/membrane-protein-research/ ************************************************************************************ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
