Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.187 

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This is version 1.5 of the entry. See complete history


Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation.

Phale, P.S.Philippsen, A.Widmer, C.Phale, V.P.Rosenbusch, J.P.Schirmer, T.

(2001) Biochemistry 40: 6319-6325

  • DOI: https://doi.org/10.1021/bi010046k
  • Primary Citation of Related Structures:  
    1HXT, 1HXU, 1HXX

  • PubMed Abstract: 

    The channel constriction of OmpF porin, a pore protein in the bacterial outer membrane, is highly charged due to the presence of three arginines (R42, R82, and R132) and two acidic residues (D113 and E117). The influence of these charges on ion conductance, ion selectivity, and voltage gating has been studied with mutants D113N/E117Q, R42A/R82A/R132A/D113N/E117Q, and V18K/G131K, which were designed to remove or add protein charge at the channel constriction. The crystal structures revealed no or only local changes compared to wild-type OmpF, thus allowing a comparative study. The single-channel conductance of the isosteric D113N/E117Q variant was found to be 2-fold reduced, and that of the pentuple mutant was 70% of the wild-type value, despite a considerably larger pore cross section. Ion selectivity was drastically altered by the mutations with cation/anion permeability ratios ranging from 1 to 12. Ion flow through these and eight other mutants, which have been characterized previously, was simulated by Brownian dynamics based on the detailed crystal structures. The calculated ion selectivity and relative channel conductance values agree well with the experimental data. This demonstrates that ion translocation through porin is mainly governed by pore geometry and charge, the two factors that are properly represented in the simulations.

  • Organizational Affiliation

    Division of Microbiology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OUTER MEMBRANE PROTEIN F340Escherichia coliMutation(s): 1 
Membrane Entity: Yes 
Find proteins for P02931 (Escherichia coli (strain K12))
Explore P02931 
Go to UniProtKB:  P02931
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02931
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.187 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.105α = 90
b = 118.105β = 90
c = 52.565γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2021-10-27
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.5: 2024-02-07
    Changes: Data collection