Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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: 90930.52 
• Atom Count: 6398 
• Residue Count: 804 
• Unique protein chains: 1

1E5D

RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS

• DOI: 10.2210/pdb1E5D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759)


• Deposited: 2000-07-24 Released: 2000-11-17 
• Deposition Author(s): 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.

---

Experimental Data Snapshot

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

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

• PubMed: 11062560 
• 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 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
• 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
• 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




---

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
Molecule	Chains	Sequence Length	Organism	Details
RUBREDOXIN\:OXYGEN OXIDOREDUCTASE	A, B	402	Desulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759)	Mutation(s): 0  Gene Names: roo EC: 1.-.-.-
Find proteins for Q9F0J6 (Desulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759)) Go to UniProtKB:  Q9F0J6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OXY	A, B	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N
FMN	A, B	FLAVIN MONONUCLEOTIDE RIBOFLAVIN MONOPHOSPHATE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
FEO	A, B	MU-OXO-DIIRON Fe2 O NPMYUMBHPJGBFA-UHFFFAOYSA-N

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 = 98.240	α = 90.00
b = 101.250	β = 90.00
c = 90.800	γ = 90.00

Software Package:

Software Name	Purpose
HKL	data scaling
SHELXL-97	phasing
SHELXL-97	refinement
HKL	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-07-24 
• Released Date: 2000-11-17 
• Deposition Author(s): 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.

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
• Version 1.3: 2018-04-18
  Type: Data collection, Database references
• Version 1.4: 2019-05-08
  Type: Data collection, Experimental preparation
• Version 1.5: 2019-05-22
  Type: Data collection, Refinement description
• Version 1.6: 2019-07-10
  Type: Data collection