4IWK

Crystal structure of iron soaked (overnight) ferritin from Pseudo-nitzschia multiseries

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

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This is version 1.2 of the entry. See complete history. 


Literature

Mechanism of ferrous iron binding and oxidation by ferritin from a pennate diatom.

Pfaffen, S., Abdulqadir, R., Le Brun, N.E., Murphy, M.E.

(2013) J Biol Chem 288: 14917-14925

  • DOI: 10.1074/jbc.M113.454496

  • PubMed Abstract: 

    • A novel ferritin was recently found in Pseudo-nitzschia multiseries (PmFTN), a marine pennate diatom that plays a major role in global primary production and carbon sequestration into the deep ocean. Crystals of recombinant PmFTN were soaked in iron and zinc solutions, and the structures were solved to 1 ...

    A novel ferritin was recently found in Pseudo-nitzschia multiseries (PmFTN), a marine pennate diatom that plays a major role in global primary production and carbon sequestration into the deep ocean. Crystals of recombinant PmFTN were soaked in iron and zinc solutions, and the structures were solved to 1.65-2.2-Å resolution. Three distinct iron binding sites were identified as determined from anomalous dispersion data from aerobically grown ferrous soaked crystals. Sites A and B comprise the conserved ferroxidase active site, and site C forms a pathway leading toward the central cavity where iron storage occurs. In contrast, crystal structures derived from anaerobically grown and ferrous soaked crystals revealed only one ferrous iron in the active site occupying site A. In the presence of dioxygen, zinc is observed bound to all three sites. Iron oxidation experiments using stopped-flow absorbance spectroscopy revealed an extremely rapid phase corresponding to Fe(II) oxidation at the ferroxidase site, which is saturated after adding 48 ferrous iron to apo-PmFTN (two ferrous iron per subunit), and a much slower phase due to iron core formation. These results suggest an ordered stepwise binding of ferrous iron and dioxygen to the ferroxidase site in preparation for catalysis and a partial mobilization of iron from the site following oxidation.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferritin
A, B, C, D, E, F
A, B, C, D, E, F
168Pseudo-nitzschia multiseriesMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE
Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth F],
G [auth A],
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth F],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth E],
X [auth E],
Y [auth E],
Z [auth E]
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
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.251α = 90
b = 126.251β = 90
c = 170.299γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description