2YCG | pdb_00002ycg

Structure of unreduced ferric cytochrome c peroxidase obtained by multicrystal method

• PDB DOI: https://doi.org/10.2210/pdb2YCG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-03-14 Released: 2011-03-30 
• Deposition Author(s): Gumiero, A., Raven, E.L., Moody, P.C.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.196 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.140 (DCC) 

Starting Model: experimental

Literature

Hydrogen Bonds in Ferric Cytochrome C Peroxidase: A Combined X-Ray and Neutron Study

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: 34.52 kDa 
• Atom Count: 3,028 
• Modeled 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, MITOCHONDRIAL	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 3 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
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.196 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.140 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.118	α = 90
b = 75.6	β = 90
c = 106.752	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-30 
Deposition Author(s): Gumiero, A., Raven, E.L., Moody, P.C.E.

Revision History  

• Version 1.0: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-08-17
  Changes: Atomic model, Derived calculations
• Version 1.2: 2019-05-22
  Changes: Data collection, Other, Refinement description
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description