3M2C | pdb_00003m2c

Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate

• PDB DOI: https://doi.org/10.2210/pdb3M2C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-03-06 Released: 2010-05-12 
• Deposition Author(s): Meharenna, Y.T., Poulos, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Work: 
  0.116 (Depositor), 0.140 (DCC) 

Literature

Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate.

Meharenna, Y.T., Doukov, T., Li, H., Soltis, S.M., Poulos, T.L.

(2010) Biochemistry 49: 2984-2986

• PubMed: 20230048 
• DOI: https://doi.org/10.1021/bi100238r
• Primary Citation of Related Structures:  
  3M23, 3M25, 3M26, 3M27, 3M28, 3M29, 3M2A, 3M2B, 3M2C, 3M2D, 3M2E, 3M2F, 3M2G, 3M2H, 3M2I


• PubMed Abstract: 
  

  The ferryl [Fe(IV)O] intermediate is important in many heme enzymes, and thus, the precise nature of the Fe(IV)-O bond is critical in understanding enzymatic mechanisms. The 1.40 A crystal structure of cytochrome c peroxidase Compound I has been determined as a function of X-ray dose while the visible spectrum was being monitored. The Fe-O bond increases in length from 1.73 A in the low-X-ray dose structure to 1.90 A in the high-dose structure. The low-dose structure correlates well with an Fe(IV) horizontal lineO bond, while we postulate that the high-dose structure is the cryo-trapped Fe(III)-OH species previously thought to be an Fe(IV)-OH species.

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Organizational Affiliation: 

Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA.

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: 34.03 kDa 
• Atom Count: 3,074 
• Modelled Residue Count: 291 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c peroxidase, mitochondrial	A	291	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: CCP, CCP1, 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 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
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Work:  0.116 (Depositor), 0.140 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.019	α = 90
b = 74.721	β = 90
c = 50.857	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SHELX	model building
SHELXL-97	refinement
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Meharenna, Y.T., Poulos, T.L.

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection