3K19

OmpF porin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.79 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of the OmpF porin crystallized in the presence of foscholine-12.

Kefala, G.Ahn, C.Krupa, M.Esquivies, L.Maslennikov, I.Kwiatkowski, W.Choe, S.

(2010) Protein Sci. 19: 1117-1125

  • DOI: 10.1002/pro.369
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The endogenous Escherichia coli porin OmpF was crystallized as an accidental by-product of our efforts to express, purify, and crystallize the E. coli integral membrane protein KdpD in the presence of foscholine-12 (FC12). FC12 is widely used in memb ...

    The endogenous Escherichia coli porin OmpF was crystallized as an accidental by-product of our efforts to express, purify, and crystallize the E. coli integral membrane protein KdpD in the presence of foscholine-12 (FC12). FC12 is widely used in membrane protein studies, but no crystal structure of a protein that was both purified and crystallized with this detergent has been reported in the Protein Data Bank. Crystallization screening for KdpD yielded two different crystals of contaminating protein OmpF. Here, we report two OmpF structures, the first membrane protein crystal structures for which extraction, purification, and crystallization were done exclusively with FC12. The first structure was refined in space group P21 with cell parameters a = 136.7 A, b = 210.5 A, c = 137 A, and beta = 100.5 degrees , and the resolution of 3.8 A. The second structure was solved at the resolution of 4.4 A and was refined in the P321 space group, with unit cell parameters a = 215.5 A, b = 215.5 A, c = 137.5 A, and gamma = 120 degrees . Both crystal forms show novel crystal packing, in which the building block is a tetrahedral arrangement of four trimers. Additionally, we discuss the use of FC12 for membrane protein crystallization and structure determination, as well as the problem of the OmpF contamination for membrane proteins overexpressed in E. coli.


    Organizational Affiliation

    Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd., La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane protein F
A, B, C, D, E, F, G, H, I, J, K, L
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: 3.79 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.280 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 136.708α = 90.00
b = 210.522β = 100.49
c = 137.042γ = 90.00
Software Package:
Software NamePurpose
BALBESphasing
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance