The problem keeps during the deposition! I tried to replace all 'HEM' atoms with the pdb published before and run refinement. The mismatch is still there. Here is a picture cut from pdb deposition website.
The 3 letter of my heme is 'HEM' which is exactly the 'PROTOPORPHYRIN IX CONTAINING FE '. I also checked the pdb CCD in which the 'HEM' image model does contain ion but not in the SMILES. My question: if this is the problem cause the mismatch, how to fix it? Thank you guys!! Bing ________________________________________ From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk] Sent: Sunday, September 14, 2014 6:16 PM To: Wang, Bing Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] ligand mismathces in pdb deposit On 12/09/14 23:28, Wang, Bing wrote: > Hi guys, Hello. > > A quick question about pdb deposition! My protein has a common ligand > 'heme' which mismatches with the ligand in pdb CCD (/Chemical > Component Dictionary/). What makes you think so? > However i didn't find any differences in it. Is that because of the > positions of double bonds or hydrogen atoms, unlikely. > since my model don't have hydrogen atoms. Actually i replace the heme > with exact one from CCD and run refmac which give me a new pdb file. > Unfortunately, CCD still didn’t recognize the heme. It is not clear to me what test you are performing. I do note that the SMILES for HEM in the CCD doesn't contain Fe - that might be related. HTH, Paul.
