JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for CCP4BB Archives


CCP4BB Archives

CCP4BB Archives


CCP4BB@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CCP4BB Home

CCP4BB Home

CCP4BB  June 2010

CCP4BB June 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Common protein crystallization contaminants

From:

"Murray, James W" <[log in to unmask]>

Reply-To:

Murray, James W

Date:

Fri, 11 Jun 2010 12:03:23 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (93 lines) , pdb_cell_scan.py (1 lines) , pdb_cells.txt.gz (1 lines)


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

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager