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CCP4BB  November 2010

CCP4BB November 2010

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Subject:

Re: DTU vs DTT ?

From:

MARTYN SYMMONS <[log in to unmask]>

Reply-To:

MARTYN SYMMONS <[log in to unmask]>

Date:

Thu, 25 Nov 2010 17:39:05 +0000

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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 <[log in to unmask]> wrote:

> From: Linda Schuldt <[log in to unmask]>
> Subject: Re: [ccp4bb] DTU vs DTT ?
> To: [log in to unmask]
> 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 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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