1E5D

RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS

PDB DOI: https://doi.org/10.2210/pdb1E5D/pdb

Classification: OXIDOREDUCTASE
Organism(s): Megalodesulfovibrio 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.248 (Depositor)
R-Value Work:
0.160 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.8 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

PubMed: 11062560 Search on PubMed
DOI: https://doi.org/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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RUBREDOXIN\:OXYGEN OXIDOREDUCTASE	A, B	402	Megalodesulfovibrio 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9F0J6
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
FEO Query on FEO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	MU-OXO-DIIRON Fe₂ O NPMYUMBHPJGBFA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.248 (Depositor)
R-Value Work: 0.160 (DCC)
R-Value Observed: 0.180 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2000-11-17

Deposition Author(s):

Rodrigues-Pousada, C.

Carrondo, M.A.

Le Gall, J.

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
Version 1.8: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other