[ccp4bb] DTU vs DTT ?
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
Re: [ccp4bb] DTU vs DTT ?
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
Re: [ccp4bb] DTU vs DTT ?
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 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
Re: [ccp4bb] DTU vs DTT ?
DTT.cif in $CLIBD_MON has explicit chiralities, assuming these are right DTT chir_01 C2 C1 O2 C3positiv DTT chir_02 C3 C2 O3 C4negativ On 25 Nov 2010, at 17:11, Paul Emsley wrote: 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 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
Re: [ccp4bb] DTU vs DTT ?
Hi Emmanuel, The monomer library is great, but it is also created by scientists (and computers) that can err. I remember a few cases (some reported on the ccp4bb) where mistakes were revealed and later fixed. Just because something is in the monomer library that does absolve anyone from not checking their ligands. And that still should not decrease our appreciation of scientists for the selfless task of creating the monomer library that ships with ccp4 and phenix. Another great resource is Gerard Kleywegt's HIC-UP. In the cases where I suspected the monomer library of having errors, HIC-UP had the right geometry. In this case, Get Monomering DTT and downloading HIC-UP's DTT give me opposite chiralities on C3. I don't know which one is true, but I suspect HIC-UP is. You can download restraint files through links (to prodrg, I believe) from HIC-UP. Cheers, Engin On 11/25/10 8:38 AM, 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 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 -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
