3M2A

Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Work: 0.116 

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This is version 1.3 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c peroxidase, mitochondrial291Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: CCPCCP1CPOYKR066C
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
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  • Reference Sequence
Small Molecules
Ligands 2 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
PO4
Query on PO4

Download Ideal Coordinates CCD File 
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 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.069α = 90
b = 74.755β = 90
c = 50.904γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHELXmodel building
SHELXL-97refinement
HKL-2000data scaling
SHELXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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