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 1.3 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: 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BACTERIOFERRITIN
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
158Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ABD3 (Escherichia coli (strain K12))
Explore P0ABD3 
Go to UniProtKB:  P0ABD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABD3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
DA [auth G]
IA [auth I]
NA [auth K]
O [auth A]
T [auth C]
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
Query on MN

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth G]
CA [auth G]
EA [auth H]
FA [auth H]
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 = 211.1α = 90
b = 211.1β = 90
c = 145.2γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other