Biological Assembly 1  

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: 90.93 kDa 
• Atom Count: 6,568 
• Modelled Residue Count: 802 
• Deposited Residue Count: 804 
• Unique protein chains: 1

 1E5D

RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS

• PDB DOI: 10.2210/pdb1E5D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfovibrio gigas
• Mutation(s): No 


• 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.

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Experimental Data Snapshot

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

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

• PubMed: 11062560 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
FEO	D [auth A], G [auth B]	MU-OXO-DIIRON Fe2 O NPMYUMBHPJGBFA-UHFFFAOYSA-N
OXY	E [auth A], H [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

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 = 98.24	α = 90
b = 101.25	β = 90
c = 90.8	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  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