Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.75 kDa 
• Atom Count: 3006 
• Modelled Residue Count: 339 
• Deposited Residue Count: 340 
• Unique protein chains: 1

2ZFG

Structure of OMPF PORIN

• PDB DOI: 10.2210/pdb2ZFG/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2008-01-04 Released: 2008-07-29 
• Deposition Author(s): Cramer, W.A., Zakharov, S.D., Yamashita, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.218 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Crystal structures of the OmpF porin: function in a colicin translocon.

Yamashita, E., Zhalnina, M.V., Zakharov, S.D., Sharma, O., Cramer, W.A.

(2008) EMBO J 27: 2171-2180

• PubMed: 18636093 
• DOI: 10.1038/emboj.2008.137
• Primary Citation of Related Structures:  
  2ZFG, 2ZLD


• PubMed Abstract: 
  

The OmpF porin in the Escherichia coli outer membrane (OM) is required for the cytotoxic action of group A colicins, which are proposed to insert their translocation and active domains through OmpF pores. A crystal structure was sought of OmpF with an inserted colicin segment. A 1.6 A OmpF structure, obtained from crystals formed in 1 M Mg2+, has one Mg2+ bound in the selectivity filter between Asp113 and Glu117 of loop 3. Co-crystallization of OmpF with the unfolded 83 residue glycine-rich N-terminal segment of colicin E3 (T83) that occludes OmpF ion channels yielded a 3.0 A structure with inserted T83, which was obtained without Mg2+ as was T83 binding to OmpF. The incremental electron density could be modelled as an extended poly-glycine peptide of at least seven residues. It overlapped the Mg2+ binding site obtained without T83, explaining the absence of peptide binding in the presence of Mg2+. Involvement of OmpF in colicin passage through the OM was further documented by immuno-extraction of an OM complex, the colicin translocon, consisting of colicin E3, BtuB and OmpF.

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein F	A	340	Escherichia coli	Mutation(s): 0  Gene Names: ompF, cmlB, coa, cry, tolF Membrane Entity: Yes
UniProt
Find proteins for P02931 (Escherichia coli (strain K12)) Explore P02931  Go to UniProtKB:  P02931

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8E	C [auth A], D [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.218 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.923	α = 90
b = 116.923	β = 90
c = 51.346	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-04 
• Released Date: 2008-07-29 
Deposition Author(s): Cramer, W.A., Zakharov, S.D., Yamashita, E.

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance