1BCF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 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.Mol.Biol. 1: 453-460


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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BACTERIOFERRITIN
A, B, C, D, E, F, G, H, I, J, K, L
158Escherichia coli (strain K12)Gene Names: bfr
EC: 1.16.3.1
Find proteins for P0ABD3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABD3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, C, E, G, I, K
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.208 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 211.100α = 90.00
b = 211.100β = 90.00
c = 145.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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