3D5K

Crystal structure of the OprM channel in a non-symmetrical space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and dynamical insights into the opening mechanism of P. aeruginosa OprM channel.

Phan, G.Benabdelhak, H.Lascombe, M.B.Benas, P.Rety, S.Picard, M.Ducruix, A.Etchebest, C.Broutin, I.

(2010) Structure 18: 507-517

  • DOI: 10.1016/j.str.2010.01.018

  • PubMed Abstract: 
  • Originally described in bacteria, drug transporters are now recognized as major determinants in antibiotics resistance. For Gram-negative bacteria, the reversible assembly consisting of an inner membrane protein responsible for the active transport, ...

    Originally described in bacteria, drug transporters are now recognized as major determinants in antibiotics resistance. For Gram-negative bacteria, the reversible assembly consisting of an inner membrane protein responsible for the active transport, a periplasmic protein, and an exit outer membrane channel achieves transport. The opening of the outer membrane protein OprM from Pseudomonas aeruginosa was modeled through normal mode analysis starting from a new X-ray structure solved at 2.4 A resolution in P2(1)2(1)2(1) space group. The three monomers are not linked by internal crystallographic symmetries highlighting the possible functional differences. This structure is closed at both ends, but modeling allowed for an opening that is not reduced to the classically proposed "iris-like mechanism."


    Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, UMR 8015 CNRS, Faculté des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris Cedex 06, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane protein oprM
A, B, C
474Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: oprM (oprK)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric
Protein: 
OprM drug discharge outer membrane protein
Find proteins for Q51487 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q51487
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SCY
Query on SCY
A, B, C
L-PEPTIDE LINKINGC5 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.900α = 90.00
b = 70.200β = 90.00
c = 344.500γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata scaling
ADSCdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-04-18
    Type: Database references