1E5D

RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.7 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 Biol 7: 1041

  • DOI: 10.1038/80961
  • Primary Citation of Related Structures:  
    1E5D

  • 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 water in a direct and safe way ...

    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: 
    • 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., LeGall, J., Dauter, Z., Wilson, K., Carrondo, M.A.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 1465
    • 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
    • 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 Commun 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RUBREDOXIN\:OXYGEN OXIDOREDUCTASEA, B402Desulfovibrio gigasMutation(s): 0 
EC: 1
UniProt
Find proteins for Q9F0J6 (Desulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759))
Explore Q9F0J6 
Go to UniProtKB:  Q9F0J6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
FEO
Query on FEO

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
OXY
Query on OXY

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.24α = 90
b = 101.25β = 90
c = 90.8γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
HKLdata reduction
HKLdata scaling
SHELXL-97phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.6: 2019-07-10
    Changes: Data collection
  • Version 1.7: 2019-07-24
    Changes: Data collection