3R99

Joint Neutron and X-ray structure of Cytochrome c peroxidase


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Hydrogen bonds in heme peroxidases: a combined X-ray and neutron study of cytochrome c peroxidase

Gumiero, A.Blakeley, M.P.Metcalfe, C.L.Murphy, E.J.Raven, E.L.Moody, P.C.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c peroxidase293Saccharomyces 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: NEUTRON DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.547α = 90
b = 76.655β = 90
c = 107.078γ = 90
Software Package:
Software NamePurpose
QLDdata collection
PHENIXmodel building
PHENIXrefinement
LAUEGENdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection
  • Version 1.2: 2018-05-16
    Changes: Data collection
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations