Hi Emmanuel,
it is hard for me to imagine that Coot has the wrong stereoisomer. So what
I think might have happend is the following:
You have imported the correct DTT, but when you have fitted the molecule
into the map you might have distorted the sterochemistry at the C3 atom.
And then it was refined like that. I had once a similar observation with
MPD. Did you insert the three DTT molecules individually, or did you "copy
and paste" the same molecule around (which might explain why you have it
for all three)?
And why donīt you just import DTT into Coot and check yourself if it has
the correct sterochemistry. This is a fast and easy way to find out if
something is wrong in your Coot library.
Unless you have very high resolution which clearly shows that you have DTU
instead of DTT, I would change your coordinate file to DTT and send it
again to the pdb.
Hope this helps you.
Best wishes,
Linda
Emmanuel Saridakis schrieb:
> Dear All,
>
> Possibly a trivial question but your experience would be much appreciated:
>
> I recently submitted a structure to PDB containing 3 DTT (dithiothreitol)
> molecules, or so I thought. The molecules had been imported and fitted
> with Coot using the Get Monomer... instruction with the code DTT. The
> Annotator responded, quite rightly as it turns out, as follows:
>
> Please note DTT in your coordinates has been changed to DTU since it
>>> has incorrect stereochemistry as DTT.
>>> Please review the stereochemistory in the attached validation report
>>> summary.
>>>
>>> You can send me corrected stereochemistry for DTT if you want it
>>> changed back.
>>>
>>> DTU (2R,3S)-1,4-disulfanylbutane-2,3-diol
>>> C4 H10 O2 S2
>>>
>>> DTT (2R,3R)-1,4-disulfanylbutane-2,3-diol
>>> C4 H10 O2 S2
>
> So, is the "DTT" monomer of Coot in fact its stereoisomer known as
> dithioerythritol? Should I import the correct DTT from elsewhere and
> re-refine or is there something else behind this?
>
> Thanks a lot for any suggestions!
>
>
> Emmanuel
>
>
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