Credit where it's due, Coot's "Get Monomer" is just a wrapper for LIBCHECK.
If you look at the restraints for DTT after Get Monomer, you will notice
that chiral centres are both marked as "both". Using the restraints
editor (or otherwise) change them to "positive" (C2) and "negative" (C3)
and everything will be fine (you may need to flip the H2 and H3
hydrogens if you have them).
If you wanted to use something other than LIBCHECK, you could search the
SBase monomers and prodrgify the result (search using the substring
"dithiobutane" (and "mercaptobutane" for DTU) incidentally).
Paul
On 25/11/10 16:38, Linda Schuldt wrote:
> 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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