8W95 | pdb_00008w95

Azumapecten Farreri homopolymeric ferritin (ApF) mutant-H2KE exposed to H2O2 for 20 s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.227 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural Insights into the Reaction between Hydrogen Peroxide and Di-iron Complexes at the Ferroxidase Center of Ferritin.

Jiao, R.Zhao, G.Zhang, T.

(2024) Inorg Chem 63: 3359-3365

  • DOI: https://doi.org/10.1021/acs.inorgchem.3c03889
  • Primary Citation Related Structures: 
    8W91, 8W92, 8W93, 8W94, 8W95, 8WB3

  • PubMed Abstract: 

    The Fe(II) oxidation mechanism in the ferroxidase center of heavy chain ferritin has been studied extensively. However, the actual production of H 2 O 2 was found to be substantially lower than expected at low flux of Fe(II) to ferritin subunits. Here, we demonstrated that H 2 O 2 could interact with the di-iron nuclear center, leading to the production of hydroxyl radicals and oxygen. Two reaction intermediates were captured in the ferroxidase center by using the time-lapse crystallographic techniques in a shellfish ferritin. The crystal structures revealed the binding of H 2 O 2 as a μ -1,2-peroxo-diferric species and the binding of O 2 to the diferric structure. This investigation sheds light on the reaction between the di-iron nuclear center and H 2 O 2 and provides insights for the exploitation of metalloenzymes.


  • Organizational Affiliation
    • Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.

Macromolecule Content 

  • Total Structure Weight: 20.16 kDa 
  • Atom Count: 1,519 
  • Modeled Residue Count: 169 
  • Deposited Residue Count: 171 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FerritinA [auth b]171Azumapecten farreriMutation(s): 2 
EC: 1.16.3.1
UniProt
Find proteins for A0A173CSP7 (Azumapecten farreri)
Explore A0A173CSP7 
Go to UniProtKB:  A0A173CSP7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A173CSP7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.641α = 90
b = 148.641β = 90
c = 148.641γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references, Structure summary