2VXI

The binding of heme and zinc in Escherichia coli Bacterioferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Binding of Haem and Zinc in the 1.9 A X-Ray Structure of Escherichia Coli Bacterioferritin.

Willies, S.C.Isupov, M.N.Garman, E.F.Littlechild, J.A.

(2009) J.Biol.Inorg.Chem. 14: 201

  • DOI: 10.1007/s00775-008-0438-8

  • PubMed Abstract: 
  • The crystal structure of Escherichia coli bacterioferritin has been solved to 1.9 A, and shows the symmetrical binding of a haem molecule on the local twofold axis between subunits and a pair of metal atoms bound to each subunit at the ferroxidase ce ...

    The crystal structure of Escherichia coli bacterioferritin has been solved to 1.9 A, and shows the symmetrical binding of a haem molecule on the local twofold axis between subunits and a pair of metal atoms bound to each subunit at the ferroxidase centre. These metals have been identified as zinc by the analysis of the structure and X-ray data and confirmed by microfocused proton-induced X-ray emission experiments. For the first time the haem has been shown to be linked to both the internal and the external environments via a cluster of waters positioned above the haem molecule.


    Organizational Affiliation

    School of Biosciences, Henry Wellcome Building for Biocatalysis, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.




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)Mutation(s): 0 
Gene Names: bfr
EC: 1.16.3.1
Find proteins for P0ABD3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABD3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
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: 1.91 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 208.100α = 90.00
b = 208.100β = 90.00
c = 142.768γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACmodel building
SHELXDphasing
REFMACphasing
DMphasing
REFMACrefinement
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance