4ZL6

Crystal structure of the PmFTN variant E44H soaked in iron (3 h)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1074/jbc.M115.669713
  • Primary Citation of Related Structures:  

  • 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 (sit ...

    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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferritin
B, A, C, D, E, F
169Pseudo-nitzschia multiseriesMutation(s): 1 
Gene Names: FTN
EC: 1.16.3.1
Find proteins for B6DMH6 (Pseudo-nitzschia multiseries)
Go to UniProtKB:  B6DMH6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D, E, F
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.167 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 126.720α = 90.00
b = 126.720β = 90.00
c = 170.310γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Database references
  • Version 1.2: 2015-12-02
    Type: Database references