4U3G

Crystal structure of Escherichia coli bacterioferritin mutant D132F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The B-type Channel Is a Major Route for Iron Entry into the Ferroxidase Center and Central Cavity of Bacterioferritin.

Wong, S.G.Grigg, J.C.Le Brun, N.E.Moore, G.R.Murphy, M.E.Mauk, A.G.

(2015) J Biol Chem 290: 3732-3739

  • DOI: https://doi.org/10.1074/jbc.M114.623082
  • Primary Citation of Related Structures:  
    4U3G

  • PubMed Abstract: 

    Bacterioferritin is a bacterial iron storage and detoxification protein that is capable of forming a ferric oxyhydroxide mineral core within its central cavity. To do this, iron must traverse the bacterioferritin protein shell, which is expected to occur through one or more of the channels through the shell identified by structural studies. The size and negative electrostatic potential of the 24 B-type channels suggest that they could provide a route for iron into bacterioferritin. Residues at the B-type channel (Asn-34, Glu-66, Asp-132, and Asp-139) of E. coli bacterioferritin were substituted to determine if they are important for iron core formation. A significant decrease in the rates of initial oxidation of Fe(II) at the ferroxidase center and subsequent iron mineralization was observed for the D132F variant. The crystal structure of this variant shows that substitution of residue 132 with phenylalanine caused a steric blockage of the B-type channel and no other material structural perturbation. We conclude that the B-type channel is a major route for iron entry into both the ferroxidase center and the iron storage cavity of bacterioferritin.


  • Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, the Centre for Blood Research and.


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 coli CFT073Mutation(s): 1 
Gene Names: bfrc4107
EC: 1.16.3.1
UniProt
Find proteins for P0ABD4 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore P0ABD4 
Go to UniProtKB:  P0ABD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABD4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth K]
BA [auth L]
M [auth A]
N [auth A]
O [auth B]
AA [auth K],
BA [auth L],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth C],
R [auth D],
S [auth E],
T [auth F],
U [auth G],
V [auth G],
W [auth H],
X [auth I],
Y [auth J],
Z [auth J]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.518α = 90
b = 208.518β = 90
c = 142.971γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CIHR/Canadian Blood ServicesCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2014-12-31
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description