4CVI

Neutron Structure of Ferric Cytochrome c Peroxidase - Deuterium exchanged at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.138 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 2.4 of the entry. See complete history


Literature

Neutron Cryo-Crystallography Captures the Protonation State of Ferryl Heme in a Peroxidase

Casadei, C.M.Gumiero, A.Metcalfe, C.L.Murphy, E.J.Basran, J.Concilio, M.G.Teixeira, S.C.M.Schrader, T.E.Fielding, A.J.Ostermann, A.Blakeley, M.P.Raven, E.L.Moody, P.C.E.

(2014) Science 345: 193

  • DOI: https://doi.org/10.1126/science.1254398
  • Primary Citation of Related Structures:  
    4CVI, 4CVJ

  • PubMed Abstract: 

    Heme enzymes activate oxygen through formation of transient iron-oxo (ferryl) intermediates of the heme iron. A long-standing question has been the nature of the iron-oxygen bond and, in particular, the protonation state. We present neutron structures of the ferric derivative of cytochrome c peroxidase and its ferryl intermediate; these allow direct visualization of protonation states. We demonstrate that the ferryl heme is an Fe(IV)=O species and is not protonated. Comparison of the structures shows that the distal histidine becomes protonated on formation of the ferryl intermediate, which has implications for the understanding of O-O bond cleavage in heme enzymes. The structures highlight the advantages of neutron cryo-crystallography in probing reaction mechanisms and visualizing protonation states in enzyme intermediates.


  • Organizational Affiliation

    Department of Biochemistry and Henry Wellcome Laboratories for Structural Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK. Institut Laue-Langevin, 71 Avenue des Martyrs, 38000, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C PEROXIDASE, MITOCHONDRIAL294Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00431
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.138 
  • Space Group: P 21 21 21
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.7α = 90
b = 76.8β = 90
c = 107.6γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
LAUEGENdata reduction
SCALAdata scaling
PHENIXphasing
PHENIXphasing
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2017-01-25
    Changes: Data collection
  • Version 2.0: 2017-06-28
    Changes: Atomic model, Refinement description
  • Version 2.1: 2017-07-05
    Changes: Data collection
  • Version 2.2: 2017-09-13
    Changes: Data collection
  • Version 2.3: 2018-06-06
    Changes: Data collection
  • Version 2.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other