1Z53

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.

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

Starting Model: experimental
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This is version 1.4 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

PubMed: 15900441 Search on PubMed
DOI: https://doi.org/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. 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.

Macromolecule Content

Total Structure Weight: 34.13 kDa
Atom Count: 3,021
Modelled Residue Count: 293
Deposited Residue Count: 294
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PP9 Query on PP9 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX C₃₄ H₃₄ N₄ O₄ FEDYMSUPMFCVOD-UJJXFSCMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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 = 106.852	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-06-21

Deposition Author(s):

Bhaskar, B.

Poulos, T.L.

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