Biological Assembly 1  

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

Global Symmetry: Octahedral - O  (3D View)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content

• Total Structure Weight: 229.02 kDa 
• Atom Count: 16212 
• Modelled Residue Count: 1872 
• Deposited Residue Count: 1896 
• Unique protein chains: 1

3E1O

Crystal structure of E. coli Bacterioferritin (BFR) with two ZN(II) ION sites at the Ferroxidase centre (ZN-BFR).

• PDB DOI: 10.2210/pdb3E1O/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-04 Released: 2009-05-05 
• Deposition Author(s): Crow, A., Lawson, T., Lewin, A., Moore, G.R., Le Brun, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.252 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Literature

Structural basis for iron mineralization by bacterioferritin

Crow, A., Lawson, T.L., Lewin, A., Moore, G.R., Le Brun, N.E.

(2009) J Am Chem Soc 131: 6808-6813

• PubMed: 19391621 
• DOI: 10.1021/ja8093444
• Primary Citation of Related Structures:  
  3E1J, 3E1L, 3E1M, 3E1N, 3E1O, 3E1P


• PubMed Abstract: 
  

Ferritin proteins function to detoxify, solubilize and store cellular iron by directing the synthesis of a ferric oxyhydroxide mineral solubilized within the protein's central cavity. Here, through the application of X-ray crystallographic and kinetic methods, we report significant new insight into the mechanism of mineralization in a bacterioferritin (BFR). The structures of nonheme iron-free and di-Fe(2+) forms of BFR showed that the intrasubunit catalytic center, known as the ferroxidase center, is preformed, ready to accept Fe(2+) ions with little or no reorganization. Oxidation of the di-Fe(2+) center resulted in a di-Fe(3+) center, with bridging electron density consistent with a mu-oxo or hydro bridged species. The mu-oxo bridged di-Fe(3+) center appears to be stable, and there is no evidence that Fe(3+)species are transferred into the core from the ferroxidase center. Most significantly, the data also revealed a novel Fe(2+) binding site on the inner surface of the protein, lying approximately 10 A directly below the ferroxidase center, coordinated by only two residues, His46 and Asp50. Kinetic studies of variants containing substitutions of these residues showed that the site is functionally important. In combination, the data support a model in which the ferroxidase center functions as a true catalytic cofactor, rather than as a pore for the transfer of iron into the central cavity, as found for eukaryotic ferritins. The inner surface iron site appears to be important for the transfer of electrons, derived from Fe(2+) oxidation in the cavity, to the ferroxidase center. Bacterioferritin may represent an evolutionary link between ferritins and class II di-iron proteins not involved in iron metabolism.

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Organizational Affiliation: 

Centre for Molecular and Structural Biochemistry, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BACTERIOFERRITIN	A, B, C, D, E, F, G, H, I, J, K, L	158	Escherichia coli K-12	Mutation(s): 0  Gene Names: bfr, b3336, JW3298 EC: 1.16.3.1
UniProt
Find proteins for P0ABD3 (Escherichia coli (strain K12)) Explore P0ABD3  Go to UniProtKB:  P0ABD3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	BA [auth D], CB [auth K], FA [auth E], Q [auth A], RA [auth H], VA [auth I]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	CA [auth E], DB [auth L], GA [auth F], JA [auth F], KA [auth G], M [auth A], NA [auth G], OA [auth H], P [auth A], R [auth B], SA [auth I], U [auth C], WA [auth J], X [auth C], Y [auth D], ZA [auth K]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	AA [auth D], AB [auth K], BB [auth K], DA [auth E], EA [auth E], EB [auth L], FB [auth L], HA [auth F], IA [auth F], LA [auth G], MA [auth G], N [auth A], O [auth A], PA [auth H], QA [auth H], S [auth B], T [auth B], TA [auth I], UA [auth I], V [auth C], W [auth C], XA [auth J], YA [auth J], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.252 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.867	α = 90
b = 207.867	β = 90
c = 142.432	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-04 
• Released Date: 2009-05-05 
Deposition Author(s): Crow, A., Lawson, T., Lewin, A., Moore, G.R., Le Brun, N.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance