Hi Bernie,
This is an issue that the REFMAC developers and the PDB are
aware of (at least at the EBI site) and that we have also encountered in a
recent deposition. The problem is that there is indeed a discrepancy between
the stereochemistry for ATP and ADP as defined in the CCP4 monomer libraries
and that defined by "Mogul" that the PDB now uses for its validation report. As
both REFMAC and PHENIX make use of the CCP4 monomer library, this will affect
the majority of depositions with the PDB, but will only have been picked up
since PDB introduced their new validation software. I therefore suspect that
almost all PDB entries for ATP/ADP would fail the new validation test.
There is a working group being set up (funded by CCP4 I believe) to address
issues of errors in the CCP4 monomer library, and this will, in time, sort out
these issues. It think that a significant number of other ligand library
entries may also contain errors.
Best wishes,
Andrew
On 27 Aug 2014, at 16:12, Bernard D Santarsiero <[email protected]> wrote:
> I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon
> submission to Acta for publication, the wwPDB validation report was run.
> Several things were flagged, including the C4-C5 bond in the adenosine moiety
> as being too long. It generally refines to 1.46-1.47A. The "ideal" distance
> in the validation report is 1.38A, and the upon review of the ATP.cif file in
> the REFMAC library, the target distance is 1.49A (and listed as a double
> bond). Clearly 1.37-1.38A is a reasonable target value. HIC-Up gives the
> target bond length as 1.404A.
>
> Where can I grab a revised ATP.cif file? I guess I'll need to re-refine all
> of my structures and re-run the validation report.
>
> BTW, I also looked at the PDB_REDO structure report for my structure, and
> can't reproduce the Rcryst and Rfree values with the same model.
>
> Bernie
> --
> Bernard D. Santarsiero
> Research Professor
> Center for Pharmaceutical Biotechnology and the
> Department of Medicinal Chemistry and Pharmacognosy
> Center for Structural Biology
> Center for Clinical and Translational Science
> University of Illinois at Chicago
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>
