4JFB

Crystal structure of OmpF in C2 with tNCS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.801 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Stubborn contaminants: influence of detergents on the purity of the multidrug ABC transporter BmrA

Wiseman, B.Kilburg, A.Chaptal, V.Reyes-Mejia, G.C.Sarwan, J.Falson, P.Jault, J.M.

(2014) PLoS ONE 9: e114864-e114864

  • DOI: 10.1371/journal.pone.0114864

  • PubMed Abstract: 
  • Despite the growing interest in membrane proteins, their crystallization remains a major challenge. In the course of a crystallographic study on the multidrug ATP-binding cassette transporter BmrA, mass spectral analyses on samples purified with six ...

    Despite the growing interest in membrane proteins, their crystallization remains a major challenge. In the course of a crystallographic study on the multidrug ATP-binding cassette transporter BmrA, mass spectral analyses on samples purified with six selected detergents revealed unexpected protein contamination visible for the most part on overloaded SDS-PAGE. A major contamination from the outer membrane protein OmpF was detected in purifications with Foscholine 12 (FC12) but not with Lauryldimethylamine-N-oxide (LDAO) or any of the maltose-based detergents. Consequently, in the FC12 purified BmrA, OmpF easily crystallized over BmrA in a new space group, and whose structure is reported here. We therefore devised an optimized protocol to eliminate OmpF during the FC12 purification of BmrA. On the other hand, an additional band visible at ∼110 kDa was detected in all samples purified with the maltose-based detergents. It contained AcrB that crystallized over BmrA despite its trace amounts. Highly pure BmrA preparations could be obtained using either a ΔacrAB E. coli strain and n-dodecyl-β-D-maltopyranoside, or a classical E. coli strain and lauryl maltose neopentyl glycol for the overexpression and purification, respectively. Overall our results urge to incorporate a proteomics-based purity analysis into quality control checks prior to commencing crystallization assays of membrane proteins that are notoriously arduous to crystallize. Moreover, the strategies developed here to selectively eliminate obstinate contaminants should be applicable to the purification of other membrane proteins overexpressed in E. coli.


    Organizational Affiliation

    Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, F-38000, Grenoble, France; CEA, DSV, IBS, F-38000, Grenoble, France; CNRS UMR5075, IBS, F-38000, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane protein F
A, B, C, D, E, F
340Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ompF (cmlB, coa, cry, tolF)
Find proteins for P02931 (Escherichia coli (strain K12))
Go to UniProtKB:  P02931
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.801 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.262 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 161.910α = 90.00
b = 110.880β = 104.46
c = 226.140γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Database references