Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 147.78 kDa 
• Atom Count: 10,686 
• Modelled Residue Count: 1,240 
• Deposited Residue Count: 1,240 
• Unique protein chains: 1

 2FL0

Oxidized (All ferric) form of the Azotobacter vinelandii bacterioferritin

• PDB DOI:  https://doi.org/10.2210/pdb2FL0/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 2006-01-05 Released: 2006-04-04 
• Deposition Author(s): Swartz, L., Kunchinskas, K., Li, H., Poulos, T.L., Lanzilotta, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.256 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

Literature

Redox-Dependent Structural Changes in the Azotobacter vinelandii Bacterioferritin: New Insights into the Ferroxidase and Iron Transport Mechanism(,).

Swartz, L., Kuchinskas, M., Li, H., Poulos, T.L., Lanzilotta, W.N.

(2006) Biochemistry 45: 4421-4428

• PubMed: 16584178 
• DOI: https://doi.org/10.1021/bi060146w
• Primary Citation of Related Structures:  
  2FKZ, 2FL0


• PubMed Abstract: 
  

In this work, we report the X-ray crystal structure of the aerobically isolated (oxidized) and the anaerobic dithionite-reduced (at pH 8.0) forms of the native Azotobacter vinelandii bacterioferritin to 2.7 and 2.0 A resolution, respectively. Iron K-edge multiple anomalous dispersion (MAD) experiments unequivocally identified the presence of three independent iron-containing sites within the protein structure. Specifically, a dinuclear (ferroxidase) site, a b-type heme site, and the binding of a single iron atom at the four-fold molecular axis of the protein shell were observed. In addition to the novel observation of iron at the four-fold pore, these data also reveal that the oxidized form of the protein has a symmetrical ferroxidase site containing two five-coordinate iron atoms. Each iron atom is ligated by four carboxylate oxygen atoms and a single histidyl nitrogen atom. A single water molecule is found within hydrogen bonding distance of the ferroxidase site that bridges the two iron atoms on the side opposite the histidine ligands. Chemical reduction of the protein under anaerobic conditions results in an increase in the average Fe-Fe distance in the ferroxidase site from approximately 3.5 to approximately 4.0 A and the loss of one of the ligands, H130. In addition, there is significant movement of the bridging water molecule and several other amino acid side chains in the vicinity of the ferroxidase site and along the D helix to the three-fold symmetry axis. In contrast to previous work, the higher-resolution data for the dithionite-reduced structure suggest that the heme may be bound in multiple conformations. Taken together, these data allow a molecular movie of the ferroxidase gating mechanism to be developed and provide further insight into the iron uptake and/or release and mineralization mechanism of bacterioferritins in general.

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Organizational Affiliation: 

Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterioferritin	A, B, C, D, E, F, G, H	155	Azotobacter vinelandii	Mutation(s): 0  Gene Names: bfr EC: 1.16.3.1
UniProt
Find proteins for P22759 (Azotobacter vinelandii) Explore P22759  Go to UniProtKB:  P22759

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	FA [auth E], NA [auth G], O [auth A], X [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
FE2	DA [auth E], EA [auth E], GA [auth F], HA [auth F], I [auth A], J [auth A], JA [auth G], K [auth A], KA [auth G], OA [auth H], P [auth B], PA [auth H], Q [auth B], R [auth B], U [auth C], V [auth C], Y [auth D], Z [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
MG	AA [auth D], BA [auth D], CA [auth D], IA [auth F], L [auth A], LA [auth G], M [auth A], MA [auth G], N [auth A], QA [auth H], S [auth B], T [auth B], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.256 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.48	α = 90
b = 124.48	β = 90
c = 285.112	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Swartz, L., Kunchinskas, K., Li, H., Poulos, T.L., Lanzilotta, W.N.

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance