Just a footnote on the MPD which you mention - correct me if I am wrong but I think we buy it as a racemic mix and so you are just as likely to get the 4R which is ligand name MRD.
That is in 189 entries in the PDB; http://www.ebi.ac.uk/pdbe-srv/view/search?Chemical_code=MRD compared with 4S-MPD which wins out at 585 entries http://www.ebi.ac.uk/pdbe-srv/view/search?Chemical_code=MPD cheers, Martyn Martyn Symmons Cambridge --- On Thu, 25/11/10, Linda Schuldt <[email protected]> wrote: > From: Linda Schuldt <[email protected]> > Subject: Re: [ccp4bb] DTU vs DTT ? > To: [email protected] > Date: Thursday, 25 November, 2010, 16:38 > 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 don´t 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 > > > > >
