1FWX

CRYSTAL STRUCTURE OF NITROUS OXIDE REDUCTASE FROM P. DENITRIFICANS

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 

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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

  • 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.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NITROUS OXIDE REDUCTASE
A, B, C, D
595Paracoccus denitrificansMutation(s): 0 
EC: 1.7.99.6
UniProt
Find proteins for Q51705 (Paracoccus denitrificans)
Explore Q51705 
Go to UniProtKB:  Q51705
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51705
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CUZ
Query on CUZ
Download Ideal Coordinates CCD File 
AA [auth D],
J [auth A],
P [auth B],
V [auth C]		(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION
Cu4 S
IGIWMDIIFLPFOP-UHFFFAOYSA-N
CUA
Query on CUA
Download Ideal Coordinates CCD File 
I [auth A],
O [auth B],
U [auth C],
Z [auth D]		DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
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
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
Q [auth C],
W [auth D]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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 = 102.595α = 90
b = 105.09β = 110.69
c = 116.696γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

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