4D5U

Structure of OmpF in I2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Two Different Centered Monoclinic Crystals of the E. Coli Outer-Membrane Protein Ompf Originate from the Same Building Block.

Chaptal, V.Kilburg, A.Flot, D.Wiseman, B.Aghajari, N.Jault, J.Falson, P.

(2016) Biochim.Biophys.Acta 1858: 326

  • DOI: 10.1016/j.bbamem.2015.11.021

  • PubMed Abstract: 
  • Macromolecule crystal formation can be divided in two major steps: 1. the formation of a nucleus and 2. the growth of this nucleus into a full mature crystal. The latter is well described and understood, while the former remains elusive due to the di ...

    Macromolecule crystal formation can be divided in two major steps: 1. the formation of a nucleus and 2. the growth of this nucleus into a full mature crystal. The latter is well described and understood, while the former remains elusive due to the difficulty to study it and is described by nucleation theories. Here we report the structure of the Escherichia coli outer membrane porin OmpF in two centered monoclinic space groups. Strikingly, the two crystals originate from the same building block, made of two trimers of OmpF interacting via their rough side. The different crystallization conditions trigger the formation of distinct arrangement of these building blocks, leading to the formation of translational non-crystallographic symmetry (tNCS) in one case, made possible by the loose lateral packing mediated by detergents. In light of nucleation theories, these results allow us to speculate that these two crystals originate from nuclei made of either clusters of building blocks, or already forming columns that later associate laterally using detergents as glue.


    Organizational Affiliation

    Drug Resistance Mechanism and Modulation team, Institut de Biologie et Chimie des Protéines (IBCP), UMR5086 CNRS/Université Lyon 1, 7 passage du Vercors, F-69367 Lyon, France. Electronic address: vincent.chaptal@ibcp.fr.




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)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
OmpF Porin
Find proteins for P02931 (Escherichia coli (strain K12))
Go to UniProtKB:  P02931
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 159.730α = 90.00
b = 115.690β = 104.95
c = 222.854γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-20
    Type: Database references