1NML

Di-haemic Cytochrome c Peroxidase from Pseudomonas nautica 617, form IN (pH 4.0)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the mechanism of Ca(2+) activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617

Dias, J.M.Alves, T.Pereira, A.S.Bourgeois, D.Moura, I.

(2004) Structure 12: 961-973

  • DOI: 10.1016/j.str.2004.03.025
  • Primary Citation of Related Structures:  1RZ5, 1RZ6

  • PubMed Abstract: 
  • Cytochrome c peroxidase (CCP) catalyses the reduction of H(2)O(2) to H(2)O, an important step in the cellular detoxification process. The crystal structure of the di-heme CCP from Pseudomonas nautica 617 was obtained in two different conformations in ...

    Cytochrome c peroxidase (CCP) catalyses the reduction of H(2)O(2) to H(2)O, an important step in the cellular detoxification process. The crystal structure of the di-heme CCP from Pseudomonas nautica 617 was obtained in two different conformations in a redox state with the electron transfer heme reduced. Form IN, obtained at pH 4.0, does not contain Ca(2+) and was refined at 2.2 A resolution. This inactive form presents a closed conformation where the peroxidatic heme adopts a six-ligand coordination, hindering the peroxidatic reaction from taking place. Form OUT is Ca(2+) dependent and was crystallized at pH 5.3 and refined at 2.4 A resolution. This active form shows an open conformation, with release of the distal histidine (His71) ligand, providing peroxide access to the active site. This is the first time that the active and inactive states are reported for a di-heme peroxidase.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction analysis of two-dependent forms of a di-haem cytochrome c peroxidase from Pseudomonas nautica
      Dias, J.M.,Bonifacio, C.,Alves, T.,Moura, J.J.G.,Moura, I.,Romao, M.J.
      (2002) Acta Crystallogr.,Sect.D 58: 697


    Organizational Affiliation

    REQUIMTE/CQFB, Departamento de QuĂ­mica, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
di-haem cytochrome c peroxidase
A
326Marinobacter hydrocarbonoclasticusN/A
Find proteins for P83787 (Marinobacter hydrocarbonoclasticus)
Go to UniProtKB:  P83787
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.457α = 90.00
b = 114.457β = 90.00
c = 90.658γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance