2IWV

Structure of the monomeric outer membrane porin OmpG in the open and closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.269 (Depositor) 
  • R-Value Work: 
    0.224 (Depositor) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the Monomeric Outer-Membrane Porin Ompg in the Open and Closed Conformation.

Yildiz, O.Vinothkumar, K.R.Goswami, P.Kuhlbrandt, W.

(2006) EMBO J 25: 3702

  • DOI: https://doi.org/10.1038/sj.emboj.7601237
  • Primary Citation of Related Structures:  
    2IWV, 2IWW

  • PubMed Abstract: 

    OmpG, a monomeric pore-forming protein from Escherichia coli outer membranes, was refolded from inclusion bodies and crystallized in two different conformations. The OmpG channel is a 14-stranded beta-barrel, with short periplasmic turns and seven extracellular loops. Crystals grown at neutral pH show the channel in the open state at 2.3 A resolution. In the 2.7 A structure of crystals grown at pH 5.6, the pore is blocked by loop 6, which folds across the channel. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel one another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues. A total of 151 ordered LDAO detergent molecules were found in the 2.3 A structure, mostly on the hydrophobic outer surface of OmpG, mimicking the outer membrane lipid bilayer, with three LDAO molecules in the open pore. In the 2.7 A structure, OmpG binds one OG and one glucose molecule as sugar substrates in the closed pore.


  • Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OUTER MEMBRANE PROTEIN G
A, B, C, D
281Escherichia coli K-12Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P76045 (Escherichia coli (strain K12))
Explore P76045 
Go to UniProtKB:  P76045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76045
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LDA
Query on LDA

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth C]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
TAM
Query on TAM

Download Ideal Coordinates CCD File 
NB [auth B]TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CB [auth B]
DD [auth C]
DF [auth D]
E [auth A]
EF [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.269 (Depositor) 
  • R-Value Work:  0.224 (Depositor) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.6α = 79.3
b = 77β = 73.4
c = 103.9γ = 74.3
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations