1FWX

CRYSTAL STRUCTURE OF NITROUS OXIDE REDUCTASE FROM P. DENITRIFICANS

PDB DOI: https://doi.org/10.2210/pdb1FWX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paracoccus denitrificans
Mutation(s): No

Deposited: 2000-09-25 Released: 2001-09-25
Deposition Author(s): Brown, K., Djinovic-Carugo, K., Haltia, T., Cabrito, I., Saraste, M., Moura, J.J., Moura, I., Tegoni, M., Cambillau, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.264
R-Value Work: 0.241
R-Value Observed: 0.263

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Revisiting the Catalytic CuZ Cluster of Nitrous Oxide (N2O) Reductase. Evidence of a Bridging Inorganic Sulfur

Brown, K., Djinovic-Carugo, K., Haltia, T., Cabrito, I., Saraste, M., Moura, J.J., Moura, I., Tegoni, M., Cambillau, C.

(2000) J Biol Chem 275: 41133-41136

PubMed: 11024061 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M008617200
Primary Citation of Related Structures:
1FWX

PubMed Abstract:
Nitrous-oxide reductases (N2OR) catalyze the two-electron reduction of N(2)O to N(2). The crystal structure of N2ORs from Pseudomonas nautica (Pn) and Paracoccus denitrificans (Pd) were solved at resolutions of 2.4 and 1.6 A, respectively. The Pn N2OR structure revealed that the catalytic CuZ center belongs to a new type of metal cluster in which four copper ions are liganded by seven histidine residues. A bridging oxygen moiety and two other hydroxide ligands were proposed to complete the ligation scheme (Brown, K., Tegoni, M., Prudencio, M., Pereira, A. S., Besson, S., Moura, J. J. G., Moura, I., and Cambillau, C. (2000) Nat. Struct. Biol. 7, 191-195). However, in the CuZ cluster, inorganic sulfur chemical determination and the high resolution structure of Pd N2OR identified a bridging inorganic sulfur instead of an oxygen. This result reconciles the novel CuZ cluster with the hitherto puzzling spectroscopic data.

Organizational Affiliation

Architecture et Fonction des Macromolécules Biologiques, UMR 6098, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France.

Macromolecule Content

Total Structure Weight: 267.83 kDa
Atom Count: 21,176
Modelled Residue Count: 2,358
Deposited Residue Count: 2,380
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITROUS OXIDE REDUCTASE	A, B, C, D	595	Paracoccus denitrificans	Mutation(s): 0 EC: 1.7.99.6 (PDB Primary Data), 1.7.2.4 (UniProt)
UniProt
Find proteins for Q51705 (Paracoccus denitrificans) Explore Q51705 Go to UniProtKB: Q51705
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q51705
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CUZ Query on CUZ Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C]	AA [auth D], J [auth A], P [auth B], V [auth C]	(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION Cu₄ S IGIWMDIIFLPFOP-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C]
CUA Query on CUA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	I [auth A], O [auth B], U [auth C], Z [auth D]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Z [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D]	F [auth A] G [auth A] H [auth A] L [auth B] M [auth B] F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C], X [auth D], Y [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D]	E [auth A], K [auth B], Q [auth C], W [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.264
R-Value Work: 0.241
R-Value Observed: 0.263
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.595	α = 90
b = 105.09	β = 110.69
c = 116.696	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2001-09-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-09-25
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description