1E5D

RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Dioxygen Reduction Enzyme from Desulfovibrio Gigas

Frazao, C.Silva, G.Gomes, C.M.Matias, P.Coelho, R.Sieker, L.Macedo, S.Liu, M.Y.Oliveira, S.Teixeira, M.Xavier, A.V.Rodrigues-Pousada, C.Carrondo, M.A.Le Gall, J.

(2000) Nat.Struct.Mol.Biol. 7: 1041

  • DOI: 10.1038/80961

  • PubMed Abstract: 
  • Desulfovibrio gigas is a strict anaerobe that contains a well-characterized metabolic pathway that enables it to survive transient contacts with oxygen. The terminal enzyme in this pathway, rubredoxin:oxygen oxidoreductase (ROO) reduces oxygen to wat ...

    Desulfovibrio gigas is a strict anaerobe that contains a well-characterized metabolic pathway that enables it to survive transient contacts with oxygen. The terminal enzyme in this pathway, rubredoxin:oxygen oxidoreductase (ROO) reduces oxygen to water in a direct and safe way. The 2.5 A resolution crystal structure of ROO shows that each monomer of this homodimeric enzyme consists of a novel combination of two domains, a flavodoxin-like domain and a Zn-beta-lactamase-like domain that contains a di-iron center for dioxygen reduction. This is the first structure of a member of a superfamily of enzymes widespread in strict and facultative anaerobes, indicating its broad physiological significance.


    Related Citations: 
    • Studies on the Redox Centres of the Terminal Oxidase from Desulfovibrio Gigas and Evidence for its Interaction with Rubredoxin
      Gomes, C.M.,Silva, G.,Oliveira, S.,Le Gall, J.,Liu, M.-Y.,Xavier, A.V.,Rodrigues-Pousada, C.,Teixeira, M.
      (1997) J.Biol.Chem. 272: 22502
    • Crystallization and Preliminary Diffraction Data Analysis of Both Single and Pseudo-Merohedrally Twinned Crystals of Rubredoxin Oxygen Oxidoreductase from Desulfovibrio Gigas
      Frazao, C.,Sieker, L.,Coelho, R.,Morais, J.,Pacheco, I.,Chen, L.,Le Gall, J.,Dauter, Z.,Wilson, K.,Carrondo, M.A.
      (1999) Acta Crystallogr.,Sect.D D55: 1465
    • Rubredoxin Oxidase, a New Flavo-Heme-Protein, is the Site of Oxygen Reduction to Water by the " Strictly Anaerobe" Desulfovibrio Gigas
      Chen, L.,Liu, M.-Y.,Le Gall, J.,Fareleira, P.,Santos, H.,Xavier, A.V.
      (1993) Biochem.Biophys.Res.Comm. 193: 100


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apartado 127, 2781-901 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUBREDOXIN\:OXYGEN OXIDOREDUCTASE
A, B
402Desulfovibrio gigasGene Names: roo
EC: 1.-.-.-
Find proteins for Q9F0J6 (Desulfovibrio gigas)
Go to UniProtKB:  Q9F0J6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
FEO
Query on FEO

Download SDF File 
Download CCD File 
A, B
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.240α = 90.00
b = 101.250β = 90.00
c = 90.800γ = 90.00
Software Package:
Software NamePurpose
HKLdata reduction
SHELXL-97refinement
SHELXL-97phasing
HKLdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance