1EBE

Laue diffraction study on the structure of cytochrome c peroxidase compound I

• PDB DOI: https://doi.org/10.2210/pdb1EBE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2001-07-25 Released: 2001-07-26 
• Deposition Author(s): Fulop, V., Phizackerley, R.P., Soltis, S.M., Clifton, I.J., Wakatsuki, S., Erman, J.E., Hajdu, J., Edwards, S.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.144 
• R-Value Observed: 0.144 

Literature

Laue Diffraction Study on the Structure of Cytochrome C Peroxidase Compound I

Fulop, V., Phizackerley, R.P., Soltis, S.M., Clifton, I.J., Wakatsuki, S., Erman, J.E., Hajdu, J., Edwards, S.L.

(1994) Structure 2: 201

• PubMed: 8069633 
• DOI: https://doi.org/10.1016/s0969-2126(00)00021-6
• Primary Citation of Related Structures:  
  1EBE


• PubMed Abstract: 
  

  Cytochrome c peroxidase from yeast is a soluble haem-containing protein found in the mitochondrial electron transport chain where it probably protects against toxic peroxides. The aim of this study was to obtain a reliable structure for the doubly oxidized transient intermediate (termed compound I) in the reaction of cytochrome c peroxidase with hydrogen peroxide. This intermediate contains a semistable free radical on Trp191, and an oxyferryl haem group.

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Organizational Affiliation: 

Oxford Centre for Molecular Sciences, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.2 kDa 
• Atom Count: 2,603 
• Modelled Residue Count: 293 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C PEROXIDASE	A	294	Saccharomyces cerevisiae	Mutation(s): 0  EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00431  Go to UniProtKB:  P00431

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
O	C [auth A]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.144 
• R-Value Observed: 0.144 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.4	α = 90
b = 76.8	β = 90
c = 51.4	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
LEAP	data reduction
LEAP	data scaling
CCP4	phasing
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-26 
Deposition Author(s): Fulop, V., Phizackerley, R.P., Soltis, S.M., Clifton, I.J., Wakatsuki, S., Erman, J.E., Hajdu, J., Edwards, S.L.

Revision History  

• Version 1.0: 2001-07-26
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Data collection
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Refinement description