4ZLW

Crystal structure of the PmFTN variant E130A soaked in iron (overnight)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Diatom Ferritin Optimized for Iron Oxidation but Not Iron Storage.

Pfaffen, S.Bradley, J.M.Abdulqadir, R.Firme, M.R.Moore, G.R.Le Brun, N.E.Murphy, M.E.

(2015) J Biol Chem 290: 28416-28427

  • DOI: https://doi.org/10.1074/jbc.M115.669713
  • Primary Citation of Related Structures:  
    4ZKH, 4ZKW, 4ZKX, 4ZL5, 4ZL6, 4ZLW, 4ZMC

  • PubMed Abstract: 

    Ferritin from the marine pennate diatom Pseudo-nitzschia multiseries (PmFTN) plays a key role in sustaining growth in iron-limited ocean environments. The di-iron catalytic ferroxidase center of PmFTN (sites A and B) has a nearby third iron site (site C) in an arrangement typically observed in prokaryotic ferritins. Here we demonstrate that Glu-44, a site C ligand, and Glu-130, a residue that bridges iron bound at sites B and C, limit the rate of post-oxidation reorganization of iron coordination and the rate at which Fe(3+) exits the ferroxidase center for storage within the mineral core. The latter, in particular, severely limits the overall rate of iron mineralization. Thus, the diatom ferritin is optimized for initial Fe(2+) oxidation but not for mineralization, pointing to a role for this protein in buffering iron availability and facilitating iron-sparing rather than only long-term iron storage.


  • Organizational Affiliation

    Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin168Pseudo-nitzschia multiseriesMutation(s): 1 
Gene Names: FTN
EC: 1.16.3.1
UniProt
Find proteins for B6DMH6 (Pseudo-nitzschia multiseries)
Explore B6DMH6 
Go to UniProtKB:  B6DMH6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6DMH6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth F],
GA [auth F],
HA [auth F],
I [auth A],
IA [auth F],
J [auth A],
JA [auth F],
K [auth A],
KA [auth G],
L [auth A],
LA [auth G],
M [auth D],
MA [auth G],
N [auth D],
NA [auth G],
O [auth D],
OA [auth G],
P [auth D],
PA [auth H],
Q [auth D],
QA [auth H],
R [auth B],
RA [auth H],
S [auth B],
SA [auth H],
T [auth B],
U [auth B],
V [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
A
B [auth D]
C [auth B]
D [auth C]
E
A,
B [auth D],
C [auth B],
D [auth C],
E,
F,
G,
H
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.051α = 90
b = 175.051β = 90
c = 175.051γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description