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 [[log in to unmask]]
Sent: Sunday, September 14, 2014 6:16 PM
To: Wang, Bing
Cc: [log in to unmask]
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.
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