3R98

Joint Neutron and X-ray structure of Cytochrome c peroxidase

• PDB DOI: https://doi.org/10.2210/pdb3R98/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-25 Released: 2012-04-04 
• Deposition Author(s): Blakeley, M.P., Fisher, S.J., Gumiero, A., Moody, P.C.E., Raven, E.L.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.212 

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

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.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 34.09 kDa 
• Atom Count: 2,584 
• Modelled Residue Count: 293 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c peroxidase	A	293	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: CCP1, CCP, CPO, YKR066C 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 1 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

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.251 
• R-Value Work: 0.207 
• R-Value Observed: 0.212 
• 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 = 51.547	α = 90
b = 76.655	β = 90
c = 107.078	γ = 90

Software Package:

Software Name	Purpose
QLD	data collection
PHENIX	model building
PHENIX	refinement
LAUEGEN	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Blakeley, M.P., Fisher, S.J., Gumiero, A., Moody, P.C.E., Raven, E.L.

Revision History  

• 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