Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 75.46 kDa 
• Atom Count: 6305 
• Modelled Residue Count: 670 
• Deposited Residue Count: 676 
• Unique protein chains: 1

2C1V

CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS - Mixed VALENCE FORM

• PDB DOI: 10.2210/pdb2C1V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Paracoccus pantotrophus
• Mutation(s): No 


• Deposited: 2005-09-21 Released: 2006-01-13 
• Deposition Author(s): Echalier, A., Fulop, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.188 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

Activation and Catalysis of the Di-Heme Cytochrome C Peroxidase from Paracoccus Pantotrophus

Echalier, A., Goodhew, C.F., Pettigrew, G.W., Fulop, V.

(2006) Structure 14: 107

• PubMed: 16407070 
• DOI: 10.1016/j.str.2005.09.011
• Primary Citation of Related Structures:  
  2C1U, 2C1V


• PubMed Abstract: 
  

Bacterial cytochrome c peroxidases contain an electron transferring (E) heme domain and a peroxidatic (P) heme domain. All but one of these enzymes are isolated in an inactive oxidized state and require reduction of the E heme by a small redox donor protein in order to activate the P heme. Here we present the structures of the inactive oxidized and active mixed valence enzyme from Paracoccus pantotrophus. Chain flexibility in the former, as expressed by the crystallographic temperature factors, is strikingly distributed in certain loop regions, and these coincide with the regions of conformational change that occur in forming the active mixed valence enzyme. On the basis of these changes, we postulate a series of events that occur to link the trigger of the electron entering the E heme from either pseudoazurin or cytochrome c(550) and the dissociation of a coordinating histidine at the P heme, which allows substrate access.

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Organizational Affiliation: 

Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DI-HAEM CYTOCHROME C PEROXIDASE	A, B	338	Paracoccus pantotrophus	Mutation(s): 0  EC: 1.11.1.5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A], D [auth A], H [auth B], I [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
EDO	F [auth A], G [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	E [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.188 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.37	α = 90
b = 141.2	β = 90
c = 51.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-21 
• Released Date: 2006-01-13 
Deposition Author(s): Echalier, A., Fulop, V.

Revision History  

• Version 1.0: 2006-01-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance