1BCF

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a unique twofold symmetric haem-binding site.

Frolow, F.Kalb, A.J.Yariv, J.

(1994) Nat Struct Biol 1: 453-460

  • DOI: 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BACTERIOFERRITINABCDEFGHIJKL158Escherichia coliMutation(s): 0 
EC: 1.16.3.1
Find proteins for P0ABD3 (Escherichia coli (strain K12))
Explore P0ABD3 
Go to UniProtKB:  P0ABD3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, C, E, G, I, K
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
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 = 211.1α = 90
b = 211.1β = 90
c = 145.2γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

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