Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 36.00 kDa 
• Atom Count: 2770 
• Residue Count: 328 
• Unique protein chains: 1

2A3T

Cu-containing nitrite reductase

• DOI: 10.2210/pdb2A3T/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodobacter sphaeroides
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-06-27 Released: 2005-08-02 
• Deposition Author(s): Jacobson, F., Guo, H., Olesen, K., Okvist, M., Neutze, R., Sjolin, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.176 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Literature

Structures of the oxidized and reduced forms of nitrite reductase from Rhodobacter sphaeroides 2.4.3 at high pH: changes in the interactions of the type 2 copper.

Jacobson, F., Guo, H., Olesen, K., Okvist, M., Neutze, R., Sjolin, L.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1190-1198

• PubMed: 16131751 
• DOI: 10.1107/S0907444905017488
• Primary Citation of Related Structures:  
  1ZV2, 2A3T


• PubMed Abstract: 
  

Nitrite reductase is an enzyme operating in the denitrification pathway which catalyses the conversion of nitrite (NO2(-)) to gaseous nitric oxide (NO). Here, crystal structures of the oxidized and reduced forms of the copper-containing nitrite reductase from Rhodobacter sphaeroides 2.4.3 are presented at 1.74 and 1.85 A resolution, respectively. Whereas the structure of the enzyme is very similar to those of other copper-containing nitrite reductases, folding as a trimer and containing two copper sites per monomer, the structures reported here enable conformational differences between the oxidized and reduced forms of the enzyme to be identified. In the type 1 copper site, a rotational perturbation of the side chain of the copper ligand Met182 occurs upon reduction. At the type 2 copper site, a dual conformation of the catalytic residue His287 is observed in the oxidized structure but is lacking in the reduced structure, such that the interactions of the oxidized type 2 copper ion can be regarded as adopting octahedral geometry. These findings shed light on the structural mechanism of the reduction of a copper-bound nitrite to nitric oxide and water.

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Organizational Affiliation: 

Department of Chemistry and Bioscience, Chalmers University, Box 462, SE-405 30 Göteborg, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A	328	Rhodobacter sphaeroides	Mutation(s): 0  Gene Names: nirK EC: 1.7.2.1
Find proteins for Q53239 (Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)) Explore Q53239  Go to UniProtKB:  Q53239

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	A	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.176 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.436	α = 90
b = 72.436	β = 90
c = 148.089	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-27 
• Released Date: 2005-08-02 
Deposition Author(s): Jacobson, F., Guo, H., Olesen, K., Okvist, M., Neutze, R., Sjolin, L.

Revision History 

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-03-07
  Changes: Advisory, Data collection