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


This is version 2.0 of the entry. See complete history. 


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
  • Primary Citation of Related Structures:  
    1QNI

  • 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 enzymes are thought to contain a CuA electron entry site, similar to that of cytochrome c oxidase, and a CuZ catalytic center ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NITROUS-OXIDE REDUCTASE
A, B, C, D, E, F
A, B, C, D, E, F
581Marinobacter nauticusMutation(s): 0 
UniProt
Find proteins for Q7SIA3 (Marinobacter nauticus)
Explore Q7SIA3 
Go to UniProtKB:  Q7SIA3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIA3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CUZ
Query on CUZ
Download Ideal Coordinates CCD File 
BA [auth E],
GA [auth F],
H [auth A],
M [auth B],
R [auth C],
BA [auth E],
GA [auth F],
H [auth A],
M [auth B],
R [auth C],
W [auth D]
(MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION
Cu4 S
IGIWMDIIFLPFOP-UHFFFAOYSA-N		 Ligand Interaction
CUA
Query on CUA
Download Ideal Coordinates CCD File 
AA [auth E],
FA [auth F],
G [auth A],
L [auth B],
Q [auth C],
AA [auth E],
FA [auth F],
G [auth A],
L [auth B],
Q [auth C],
V [auth D]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
CA [auth E],
EA [auth E],
HA [auth F],
I [auth A],
JA [auth F],
CA [auth E],
EA [auth E],
HA [auth F],
I [auth A],
JA [auth F],
K [auth A],
N [auth B],
P [auth B],
S [auth C],
U [auth C],
X [auth D],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
DA [auth E],
IA [auth F],
J [auth A],
O [auth B],
T [auth C],
DA [auth E],
IA [auth F],
J [auth A],
O [auth B],
T [auth C],
Y [auth D]
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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