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 [[log in to unmask]]
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>
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