1BCF | pdb_00001bcf

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 (Depositor) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1BCF

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 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.

Macromolecule Content 

  • Total Structure Weight: 227.23 kDa 
  • Atom Count: 15,846 
  • Modeled Residue Count: 1,896 
  • Deposited Residue Count: 1,896 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 
EC: 1.16.3.1
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
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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 (Depositor) 
  • R-Value Observed: 0.208 (Depositor) 
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