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 

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 64: 880-885

  • DOI: 10.1107/S1744309108028248

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acriflavine resistance protein B
A
1049Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acrB (acrE)
Find proteins for P31224 (Escherichia coli (strain K12))
Go to UniProtKB:  P31224
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
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 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 145.740α = 90.00
b = 145.740β = 90.00
c = 514.000γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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