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 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    2VXI

  • 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 centre ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BACTERIOFERRITIN
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
158Escherichia coli BL21Mutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
FA [auth D],
FB [auth I],
KA [auth E],
KB [auth J],
M [auth A],
FA [auth D],
FB [auth I],
KA [auth E],
KB [auth J],
M [auth A],
PB [auth K],
QA [auth F],
S [auth B],
UA [auth G],
UB [auth L],
Z [auth C],
ZA [auth H]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth C],
CB [auth H],
DA [auth C],
DB [auth H],
EA [auth C],
CA [auth C],
CB [auth H],
DA [auth C],
DB [auth H],
EA [auth C],
EB [auth H],
IA [auth D],
IB [auth I],
JA [auth D],
JB [auth I],
NA [auth E],
NB [auth J],
OA [auth E],
OB [auth J],
P [auth A],
PA [auth E],
Q [auth A],
R [auth A],
SB [auth K],
TA [auth F],
TB [auth K],
V [auth B],
W [auth B],
X [auth B],
XA [auth G],
XB [auth L],
Y [auth B],
YA [auth G],
YB [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C],
AB [auth H],
BA [auth C],
BB [auth H],
GA [auth D],
AA [auth C],
AB [auth H],
BA [auth C],
BB [auth H],
GA [auth D],
GB [auth I],
HA [auth D],
HB [auth I],
LA [auth E],
LB [auth J],
MA [auth E],
MB [auth J],
N [auth A],
O [auth A],
QB [auth K],
RA [auth F],
RB [auth K],
SA [auth F],
T [auth B],
U [auth B],
VA [auth G],
VB [auth L],
WA [auth G],
WB [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 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 
  • R-Value Observed: 0.179 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.1α = 90
b = 208.1β = 90
c = 142.768γ = 90
Software Package:
Software NamePurpose
REFMACmodel building
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMphasing
REFMACphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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