4D5U

Structure of OmpF in I2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1016/j.bbamem.2015.11.021
  • Primary Citation of Related Structures:  
    4D5U

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OUTER MEMBRANE PROTEIN F
A, B, C, D, E
A, B, C, D, E, F
340Escherichia coli K-12Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.73α = 90
b = 115.69β = 104.95
c = 222.854γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-20
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description