1Z53

The 1.13 Angstrom Structure of Iron-free Cytochrome c Peroxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The 1.13-A structure of iron-free cytochrome c peroxidase.

Bhaskar, B.Poulos, T.L.

(2005) J Biol Inorg Chem 10: 425-430

  • DOI: 10.1007/s00775-005-0654-4
  • Primary Citation of Related Structures:  
    1Z53

  • PubMed Abstract: 
  • The iron-free cytochrome c peroxidase (CCP) crystal structure has been determined to 1.13 A and compared with the 1.2-A ferric-CCP structure. Quite unexpectedly, removal of the iron has no effect on porphyrin geometry and distortion, indicating that protein-porphyrin interactions and not iron coordination or formation of the axial His-Fe bond determines porphyrin conformation ...

    The iron-free cytochrome c peroxidase (CCP) crystal structure has been determined to 1.13 A and compared with the 1.2-A ferric-CCP structure. Quite unexpectedly, removal of the iron has no effect on porphyrin geometry and distortion, indicating that protein-porphyrin interactions and not iron coordination or formation of the axial His-Fe bond determines porphyrin conformation. However, there are changes in solvent structure in the distal pocket, which lead to changes in the distal His52 acid-base catalyst. The observed ability of His52 to move in response to small changes in solvent structure is very likely important for its role as a catalyst in assisting in the heterolytic fission of the peroxide O-O bond.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry and the Center in Chemical and Structural Biology, University of California, Irvine, CA 92697-3900, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c peroxidase, mitochondrialA294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CCP1CCPCPO
EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PP9
Query on PP9

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX
C34 H34 N4 O4
FEDYMSUPMFCVOD-UJJXFSCMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.852α = 90
b = 75.736β = 90
c = 51.041γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance