[ccp4bb] Identifying an unknown ligand
Hi, I am refining a structure and have a region of unmodeled density into which I am trying to fit a ligand. The identity of the ligand is not obvious, so I modeled a bunch of dummy atoms into the density. Could you please have a look at the map and pdb files and help me identify this ligand? Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292
Re: [ccp4bb] Identifying an unknown ligand
Some context would be helpful (essential?). What's in the crystallization solution? What, if anything, is known about the protein of interest? What is the ligand interacting with (metal ions, hydrogen bonding donors/acceptors, charged residues, etc?), and what are the interaction distances? Do any of the atoms appear to be "heavy" or show anomalous scattering, if applicable, at the wavelength used? etc. etc. -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu Abhinav Kumar wrote: Hi, I am refining a structure and have a region of unmodeled density into which I am trying to fit a ligand. The identity of the ligand is not obvious, so I modeled a bunch of dummy atoms into the density. Could you please have a look at the map and pdb files and help me identify this ligand? Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292
Re: [ccp4bb] Identifying an unknown ligand
My money is on: Dithiothreitol or dithioerythritol. Any chance they are in there? If not and you believe this copurified with your protein, than I'd guess erythritol or threitol. (I didn't bother trying to gauge the stereochemistry from your picture) Cheers Andy On 4/2/09 1:38 PM, Abhinav Kumar abhin...@slac.stanford.edu wrote: Hi, I am refining a structure and have a region of unmodeled density into which I am trying to fit a ligand. The identity of the ligand is not obvious, so I modeled a bunch of dummy atoms into the density. Could you please have a look at the map and pdb files and help me identify this ligand? Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 -- Andrew M. Gulick, Ph.D. --- (716) 898-8619 Hauptman-Woodward Institute 700 Ellicott St Buffalo, NY 14203 --- Hauptman-Woodward Institute Dept. of Structural Biology, SUNY at Buffalo http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html http://labs.hwi.buffalo.edu/gulick
Re: [ccp4bb] Identifying an unknown ligand
Some more info about this structure: Crystallization conditions: Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000, 0.1M TRIS pH 8.5 This does not sit on any crystalllographic symmetry axis. But it sits right between two monomers and the NCS 2-fold axis. The protein is chemotaxis protein CheX. Environment: Some main chain amide Ns around it, as well as phobic side chains. No peak in anomalous difference fourier map. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Abhinav Kumar wrote: Hi, I am refining a structure and have a region of unmodeled density into which I am trying to fit a ligand. The identity of the ligand is not obvious, so I modeled a bunch of dummy atoms into the density. Could you please have a look at the map and pdb files and help me identify this ligand? Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292
Re: [ccp4bb] Identifying an unknown ligand
Looks like oxalate with two water molecules nearby. Oxalate is a fairly common product of PEG oxidation. Artem --- When the Weasel comes to give New Year's greetings to the Chickens no good intentions are in his mind. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Abhinav Kumar Sent: Thursday, April 02, 2009 1:51 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Identifying an unknown ligand Some more info about this structure: Crystallization conditions: Glycerol, 0.1700M NaOAc, 25.5000% PEG-4000, 0.1M TRIS pH 8.5 This does not sit on any crystalllographic symmetry axis. But it sits right between two monomers and the NCS 2-fold axis. The protein is chemotaxis protein CheX. Environment: Some main chain amide Ns around it, as well as phobic side chains. No peak in anomalous difference fourier map. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 Abhinav Kumar wrote: Hi, I am refining a structure and have a region of unmodeled density into which I am trying to fit a ligand. The identity of the ligand is not obvious, so I modeled a bunch of dummy atoms into the density. Could you please have a look at the map and pdb files and help me identify this ligand? Please see http://smb.slac.stanford.edu/~abhinavk/UNL/unl.html Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292
