1QNI

Crystal Structure of Nitrous Oxide Reductase from Pseudomonas nautica, at 2.4A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

wwPDB Validation 3D Report Full Report



Literature

A novel type of catalytic copper cluster in nitrous oxide reductase.

Brown, K.Tegoni, M.Prudencio, M.Pereira, A.S.Besson, S.Moura, J.J.Moura, I.Cambillau, C.

(2000) Nat Struct Biol 7: 191-195

  • DOI: 10.1038/73288
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nitrous oxide (N20) is a greenhouse gas, the third most significant contributor to global warming. As a key process for N20 elimination from the biosphere, N20 reductases catalyze the two-electron reduction of N20 to N2. These 2 x 65 kDa copper enzym ...

    Nitrous oxide (N20) is a greenhouse gas, the third most significant contributor to global warming. As a key process for N20 elimination from the biosphere, N20 reductases catalyze the two-electron reduction of N20 to N2. These 2 x 65 kDa copper enzymes are thought to contain a CuA electron entry site, similar to that of cytochrome c oxidase, and a CuZ catalytic center. The copper anomalous signal was used to solve the crystal structure of N20 reductase from Pseudomonas nautica by multiwavelength anomalous dispersion, to a resolution of 2.4 A. The structure reveals that the CuZ center belongs to a new type of metal cluster, in which four copper ions are liganded by seven histidine residues. N20 binds to this center via a single copper ion. The remaining copper ions might act as an electron reservoir, assuring a fast electron transfer and avoiding the formation of dead-end products.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UPR 9039, CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITROUS-OXIDE REDUCTASEA, B, C, D, E, F581Marinobacter hydrocarbonoclasticusMutation(s): 0 
Find proteins for Q7SIA3 (Marinobacter hydrocarbonoclasticus)
Explore Q7SIA3 
Go to UniProtKB:  Q7SIA3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CUZ
Query on CUZ

Download CCD File 
A, B, C, D, E, F
(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION
Cu4 S
IGIWMDIIFLPFOP-UHFFFAOYSA-N
 Ligand Interaction
CUA
Query on CUA

Download CCD File 
A, B, C, D, E, F
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.29α = 90
b = 211.29β = 90
c = 166.457γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-06-26
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Other