Re: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes
Hi Jeremy, Given the large number of different kinds of ligands that are observed (either from crystallization, purification conditions or endogenous), I think it will be really difficult to assign just by visual and manual comparison with a standard set, especially for inexperienced crystallographers. Better to use modules like LigandFit in Phenix, which can use the Refmac ligand library or user-defined library to scan the putative ligand density in difference maps in the structure. If you want a nice overview of different common ligands that have been observed in ~3000 structures from PSI/Structural Genomics efforts (including a whole bunch of unidentified ligands), along with their PDB ids so you can see corresponding density, have a look at this paper: Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1309-16. doi: 10.1107/S1744309110008092. Epub 2010 Jul 6. Ligands in PSI structures. Kumar A, Chiu HJ, Axelrod HL, Morse A, Elsliger MA, Wilson IA, Deacon A. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA. PMID: 20944227 http://www.ncbi.nlm.nih.gov/pubmed/20944227 Best, Debanu. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ??? Sent: Tuesday, May 21, 2013 12:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes hi all, Sorry if this has been asked before. I wonder if there is an list or library of most commonly co-crystallized ligands(or solvent molecules) available? Better if the electron density maps of the ligands are also shown with different resolutions. That could help a lot for an inexperienced crystallographer (like me) to quickly identify extra electron densities in a new structure, by simply comparing the electron density shapes. I remember a few days ago somebody asked about a PEG electron density, which looks like a string of beads. If I knew that earlier, I could have modeled it in, instead of waters... Thanks, Jeremy
Re: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes
Top 20 HETNAM entries based on 58,469 PDB entries at better than 2.5 Angstrom resolution (arbitrary cut): Number of entries in histogram: 14864 Total number of instances : 195481 0 14502 0.0742 GOL(glycerol) 1 10952 0.0560 SO4 2 8064 0.0413 ZN 3 7628 0.0390 MG 4 6930 0.0355 MSE (SeMet) 5 6685 0.0342 CA 6 6555 0.0335 EDO (Ethylene glycol) 7 6315 0.0323 CL 8 5856 0.0300 HEM 9 3922 0.0201 NA 10 3647 0.0187 NAG 11 3148 0.0161 PO4 12 2360 0.0121 ACT(Acetate) 13 1874 0.0096 MN 14 1561 0.0080 NAP 15 1387 0.0071 K 16 1338 0.0068 FAD 17 1277 0.0065 PLP (PYRIDOXAL-5'-PHOSPHATE) 18 1228 0.0063 TRS(Tris buffer) 19 1205 0.0062 FMN (numeric columns are ranking; count; frequency) No electron density, sorry. Clearly I should be adding more glycerols. Phil Jeffrey Princeton From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 孙庆祥 [baby_ten...@163.com] Sent: Tuesday, May 21, 2013 3:29 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes hi all, Sorry if this has been asked before. I wonder if there is an list or library of most commonly co-crystallized ligands(or solvent molecules) available? Better if the electron density maps of the ligands are also shown with different resolutions. That could help a lot for an inexperienced crystallographer (like me) to quickly identify extra electron densities in a new structure, by simply comparing the electron density shapes. I remember a few days ago somebody asked about a PEG electron density, which looks like a string of beads. If I knew that earlier, I could have modeled it in, instead of waters... Thanks, Jeremy
Re: [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes
I'm not sure that a library of ligand electron density would be an entirely good thing. I guess something small like an acetate or DMSO would be relatively consistent but larger things like PEGS or even glycerols are going to be dependent on the nature of the binding site. A good example would be to look at something that binds ATP as an enzymatic co-factor versus a binding protein. Completely different geometry. For a beginner I'd suggest to always check your difference peaks and all your waters between rounds of refinement. If the positive density peaks are covalent bond distance apart, it's not a water. If you've got giant green smears between or around your waters it might not be a water. If you've got good enough density and can guess at a basic framework you can plug a rough sketch into the chemical structure search function in PubChem that can give you some possible options. You can cross-reference the hits to the HIC-Up server or the PDB for restraints or density examples keeping in mind that your ligand-protein interactions may be different. Also do a sanity check and ask yourself does this make chemical sense? If you've modeled something in there is TWILIGHT to see if your density supports your model. Of course there is also experimental evidence but that's a different can of worms. Basically really look at your data and if something seems hinky then look for alternatives. My $0.02, Katherine On Tue, May 21, 2013 at 3:05 PM, Jeffrey, Philip D. pjeff...@princeton.eduwrote: Top 20 HETNAM entries based on 58,469 PDB entries at better than 2.5 Angstrom resolution (arbitrary cut): Number of entries in histogram: 14864 Total number of instances : 195481 0 14502 0.0742 GOL(glycerol) 1 10952 0.0560 SO4 2 8064 0.0413 ZN 3 7628 0.0390 MG 4 6930 0.0355 MSE (SeMet) 5 6685 0.0342 CA 6 6555 0.0335 EDO (Ethylene glycol) 7 6315 0.0323 CL 8 5856 0.0300 HEM 9 3922 0.0201 NA 10 3647 0.0187 NAG 11 3148 0.0161 PO4 12 2360 0.0121 ACT(Acetate) 13 1874 0.0096 MN 14 1561 0.0080 NAP 15 1387 0.0071 K 16 1338 0.0068 FAD 17 1277 0.0065 PLP (PYRIDOXAL-5'-PHOSPHATE) 18 1228 0.0063 TRS(Tris buffer) 19 1205 0.0062 FMN (numeric columns are ranking; count; frequency) No electron density, sorry. Clearly I should be adding more glycerols. Phil Jeffrey Princeton *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 孙庆祥 [ baby_ten...@163.com] *Sent:* Tuesday, May 21, 2013 3:29 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] list/library of most commonly co-crystallized ligands/solvents and/or their electron density shapes hi all, Sorry if this has been asked before. I wonder if there is an list or library of most commonly co-crystallized ligands(or solvent molecules) available? Better if the electron density maps of the ligands are also shown with different resolutions. That could help a lot for an inexperienced crystallographer (like me) to quickly identify extra electron densities in a new structure, by simply comparing the electron density shapes. I remember a few days ago somebody asked about a PEG electron density, which looks like a string of beads. If I knew that earlier, I could have modeled it in, instead of waters... Thanks, Jeremy
