Dear All, >Re the python script to compare a unit cell to those in the PDB.
>Can you give instructions on how to run your script? put the script and the gunzipped datafile somewhere in your PATH, edit the script to point to the datafile. Run the script with the 6 cell dimensions on the command line. If your angles are all 90degrees you can omit them. pdb_cell_scan.py 78.3 78.3 38.23 90 90 90 The output is the top 10 closest pdb cells (on cell edge and angle), lower scores are closer. Test Cell 67.69 46.78 151.31 90.0 90.0 90.0 PDB score cell ---------------------------------------------------- 1tre 0.0 67.69 46.78 151.31 90.0 90.0 90.0 3cn7 103.779749 65.649 50.548 142.548 90.0 92.94 90.0 2d3w 124.666694 78.529 46.677 149.318 90.0 91.79 90.0 1gpl 179.2266 62.0 55.9 144.0 90.0 93.2 90.0 2d8o 218.984637 57.144 57.144 151.905 90.0 90.0 90.0 2d8p 219.224203 57.727 57.727 150.955 90.0 90.0 90.0 2vi2 219.704808 57.908 57.908 150.88 90.0 90.0 90.0 3e0a 219.957141 57.926 57.926 150.687 90.0 90.0 90.0 2oqn 220.041464 57.968 57.968 150.716 90.0 90.0 90.0 2g4y 220.3449 57.9 57.9 150.39 90.0 90.0 90.0 best wishes James -- Dr. James W. Murray David Phillips Research Fellow Division on Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 ________________________________________ From: Chris Ulens [[email protected]] Sent: Friday, June 11, 2010 12:56 PM To: Murray, James W Subject: Re: [ccp4bb] Common protein crystallization contaminants Very useful, thanks! Can you give instructions on how to run your script? -Chris On Jun 11, 2010, at 1:03 PM, Murray, James W wrote: Dear All, Re: Common protein crystallization contaminants thank you for all your responses. There is some literature on E. coli proteins, summarised below with other miscellaneous examples. Miscellaneous contaminants mentioned include aspartate carbamoyl transferase, triose phosphate isomerase from E. coli and ferritins from insect cells. I have written a short python script that will compare a unit cell with the cells in the PDB and return the 10 closest matches. (Script and gzipped datafile attached). This would have saved me hours of data collection and model-building on my last synchrotron trip. (NB. alternative cells and permutations of axes are not accounted for) best wishes James Summary of responses: http://www.ncbi.nlm.nih.gov/pubmed/16814929 Biochim Biophys Acta. 2006 Sep;1760(9):1304-13. Structural analysis and classification of native proteins from E. coli commonly co-purified by immobilised metal affinity chromatography. Bolanos-Garcia VM, Davies OR. Ferric uptake regulator (Fur) Metal-binding lipocalin (YodA) Cu/Zn-superoxide dismutase (Cu/Zn-SODM) Acetylornithinase (ArgE) Glycogen synthase (GlgA) Carbonic anhydrase (YadF) Glucosamine-6-phosphate synthase (GlmS) cAMP-regulatory protein (CRP) Host factor-I protein (Hfq) Chloramphenicol-O-acetyl transferase (CAT) Peptidoylproline cis–trans isomerase (SlyD) Regulatory ribosomal protein (S15) Formyl transferase (YfbG) Glucose-6-phosphate 1-dehydrogenase (G6PD) GroEL/Hsp60 Component 1 of the 2-oxoglutarate dehydrogenase complex (ODO1) Component E2 of the dihydrolipoamide succinyltransferase (ODO2) Glucose-6-phosphate 1-dehydrogenase (G6PD) Glucose-6-phosphate 1-dehydrogenase (G6PD) http://www.ncbi.nlm.nih.gov/pubmed/17554162 Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jun 1;63(Pt 6): 457-61. Epub 2007 May 5. Purification, crystallization and structure determination of native GroEL from Escherichia coli lacking bound potassium ions. Kiser PD, Lodowski DT, Palczewski K. Carbonic anhydrase (1T75) http://www.rcsb.org/pdb/explore/explore.do?structureId=1T75 Catabolite gene activator (cAMP receptor protein) http://www.ncbi.nlm.nih.gov/protein/P03020?report=genpept Polymyxin resistance protein PmrI http://www.ncbi.nlm.nih.gov/protein/6176575 inorganic pyrophosphatase lac repressor More proteins are mentioned in this paper. http://www.ncbi.nlm.nih.gov/pubmed/19887109 Protein Expr Purif. 2010 Apr;70(2):191-5. Epub 2009 Nov 1. Identification and characterization of native proteins of Escherichia coli BL-21 that display affinity towards Immobilized Metal Affinity Chromatography and Hydrophobic Interaction Chromatography Matrices. Tiwari N, Woods L, Haley R, Kight A, Goforth R, Clark K, Ataai M, Henry R, Beitle R. For membrane proteins purified from E. coli AcrB can be a problem, as well as ferritins, Omp porins and succinate dehydrogenase. http://www.ncbi.nlm.nih.gov/pubmed/19162196 J Struct Biol. 2009 Apr;166(1):107-11. AcrB et al.: Obstinate contaminants in a picogram scale. One more bottleneck in the membrane protein structure pipeline. http://www.ncbi.nlm.nih.gov/pubmed/18931428 Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Oct 1;64(Pt 10): 880-5. There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization. http://www.ncbi.nlm.nih.gov/pubmed/19770503 Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1062-73. Effects of impurities on membrane-protein crystallization in different systems. Kors CA, Wallace E, Davies DR, Li L, Laible PD, Nollert P. -- Dr. James W. Murray David Phillips Research Fellow Division on Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895<pdb_cell_scan.py><pdb_cells.txt.gz>
