1Z53 | pdb_00001z53

The 1.13 Angstrom Structure of Iron-free Cytochrome c Peroxidase

• PDB DOI: https://doi.org/10.2210/pdb1Z53/pdb

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


• Deposited: 2005-03-17 Released: 2005-06-21 
• Deposition Author(s): Bhaskar, B., Poulos, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.177 (Depositor), 0.137 (DCC) 
• R-Value Work: 
  0.147 (Depositor) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

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

• PubMed: 15900441 
• DOI: https://doi.org/10.1007/s00775-005-0654-4
• Primary Citation 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. 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.

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.13 kDa 
• Atom Count: 3,021 
• 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  Gene Names: CCP1, CCP, CPO 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
PP9	B [auth A]	PROTOPORPHYRIN IX C34 H34 N4 O4 FEDYMSUPMFCVOD-UJJXFSCMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.177 (Depositor), 0.137 (DCC) 
• R-Value Work:  0.147 (Depositor) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.852	α = 90
b = 75.736	β = 90
c = 51.041	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-21 
Deposition Author(s): Bhaskar, B., Poulos, T.L.

Revision History  

• 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
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description