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: 227.23 kDa 
• Atom Count: 15,846 
• Modelled Residue Count: 1,896 
• Deposited Residue Count: 1,896 
• Unique protein chains: 1

 1BCF

THE STRUCTURE OF A UNIQUE, TWO-FOLD SYMMETRIC, HAEM-BINDING SITE

• PDB DOI:  https://doi.org/10.2210/pdb1BCF/pdb

• Classification: IRON STORAGE AND ELECTRON TRANSPORT
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1993-12-06 Released: 1994-12-20 
• Deposition Author(s): Frolow, F., Kalb(Gilboa), A.J., Yariv, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Structure of a unique twofold symmetric haem-binding site.

Frolow, F., Kalb, A.J., Yariv, J.

(1994) Nat Struct Biol 1: 453-460

• PubMed: 7664064 
• DOI: https://doi.org/10.1038/nsb0794-453
• Primary Citation of Related Structures:  
  1BCF


• PubMed Abstract: 
  

Bacterioferritin of Escherichia coli, also known as cytochrome b1, is a hollow, nearly spherical shell made up of 24 identical protein subunits and 12 haems. We have solved this structure in a tetragonal crystal form at 2.9 A resolution. We find that each haem is bound in a pocket formed by the interface between a pair of symmetry-related subunits. The quasi-twofold axis of the haem is closely aligned with the local twofold axis relating these subunits. The axial ligands of the haem are sulphurs of two equivalent methionyl residues (Met 52) from the symmetry-related subunits. A cluster of four water molecules is trapped in the gap between the upper edge of the haem and two extended protein loops which close off the haem from the outer aqueous environment. This is the first structure of a bis-methionine ligated haem-binding site and the first case of a twofold symmetric haem-binding site.

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Related Citations: 

• Location of Haem in Bacterioferritin of Escherichia Coli
  Frolow, F., Kalb(Gilboa), A.J., Yariv, J.
  (1993) Acta Crystallogr D Biol Crystallogr 49: 597

• Amino Acid Sequence of the Bacterioferritin (Cytochrome B1) of Escherichia Coli-K12
  Andrews, S.C., Smith, J.M.A., Guest, J.R., Harrison, P.M.
  (1989) Biochem Biophys Res Commun 158: 489

• Molecular Size and Symmetry of the Bacterioferritin of Escherichia Coli: X-Ray Crystallographic Characterization of Four Crystal Forms
  Smith, J.M.A., Ford, G.C., Harrison, P.M., Yariv, J., Kalb(Gilboa), A.J.
  (1989) J Mol Biol 205: 465

• The Identity of Bacterioferritin and Cytochrome B1
  Yariv, J.
  (1983) Biochem J 211: 527

• The Composition and the Structure of Bacterioferritin of Escherichia Coli
  Yariv, J., Kalb(Gilboa), A.J., Sperling, R., Bauminger, E.R., Cohen, S.G., Ofer, S.
  (1981) Biochem J 197: 171

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Organizational Affiliation: 

Department of Chemical Services, Weizmann Institute of Science, Rehovot, Israel.

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	Mutation(s): 0  EC: 1.16.3.1
UniProt
Find proteins for P0ABD3 (Escherichia coli (strain K12)) Explore P0ABD3  Go to UniProtKB:  P0ABD3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.1	α = 90
b = 211.1	β = 90
c = 145.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-12-20 
Deposition Author(s): Frolow, F., Kalb(Gilboa), A.J., Yariv, J.

Revision History  

• Version 1.0: 1994-12-20
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance