3D9B

Symmetric structure of E. coli AcrB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.355 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization.

Veesler, D.Blangy, S.Cambillau, C.Sciara, G.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 880-885

  • DOI: 10.1107/S1744309108028248
  • Primary Citation of Related Structures:  
    3D9B

  • PubMed Abstract: 
  • In the course of a crystallographic study of the Methanosarcina mazei CorA transporter, the membrane protein was obtained with at least 95% purity and was submitted to crystallization trials. Small crystals (<100 microm) were grown that diffracted to 3.42 A resolution and belonged to space group R32, with unit-cell parameters a = b = 145 ...

    In the course of a crystallographic study of the Methanosarcina mazei CorA transporter, the membrane protein was obtained with at least 95% purity and was submitted to crystallization trials. Small crystals (<100 microm) were grown that diffracted to 3.42 A resolution and belonged to space group R32, with unit-cell parameters a = b = 145.74, c = 514.0 A. After molecular-replacement attempts using available CorA structures as search models failed to yield a solution, it was discovered that the crystals consisted of an Escherichia coli contaminating protein, acriflavine resistance protein B (AcrB), that was present at less than 5% in the protein preparations. AcrB contamination is a major problem when expressing membrane proteins in E. coli since it binds naturally to immobilized metal-ion affinity chromatography (IMAC) resins. Here, the structure is compared with previously deposited AcrB structures and strategies are proposed to avoid this contamination.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, CNRS et Universités d'Aix-Marseille I et II, UMR 6098, Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 9, France. david.veesler@afmb.univ-mrs.fr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acriflavine resistance protein BA1049Escherichia coli BL21(DE3)Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P31224 (Escherichia coli (strain K12))
Explore P31224 
Go to UniProtKB:  P31224
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.355 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.74α = 90
b = 145.74β = 90
c = 514γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references