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
