1NIR

OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA

• PDB DOI:  https://doi.org/10.2210/pdb1NIR/pdb

• Classification: NITRITE REDUCTASE
• Organism(s): Pseudomonas aeruginosa
• Mutation(s): No 


• Deposited: 1997-06-17 Released: 1997-12-03 
• Deposition Author(s): Nurizzo, D., Tegoni, M., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.242 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa.

Nurizzo, D., Silvestrini, M.C., Mathieu, M., Cutruzzola, F., Bourgeois, D., Fulop, V., Hajdu, J., Brunori, M., Tegoni, M., Cambillau, C.

(1997) Structure 5: 1157-1171

• PubMed: 9331415 
• DOI: https://doi.org/10.1016/s0969-2126(97)00267-0
• Primary Citation of Related Structures:  
  1NIR


• PubMed Abstract: 
  

Nitrite reductase from Pseudomonas aeruginosa (NiR-Pa) is a dimer consisting of two identical 60 kDa subunits, each of which contains one c and one d1 heme group. This enzyme, a soluble component of the electron-transfer chain that uses nitrate as a source of energy, can be induced by the addition of nitrate to the bacterial growth medium. NiR-Pa catalyzes the reduction of nitrite (NO2-) to nitric oxide (NO); in vitro, both cytochrome c551 and azurin are efficient electron donors in this reaction. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere.

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Organizational Affiliation: 

Architecture et Fonction des Macromolécules Biologiques, U.P.R. 9039-C.N.R.S., I.B.S.M., Marseille, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 123.47 kDa 
• Atom Count: 9,483 
• Modelled Residue Count: 1,077 
• Deposited Residue Count: 1,086 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITRITE REDUCTASE	A, B	543	Pseudomonas aeruginosa	Mutation(s): 0  EC: 1.9.3.2 (PDB Primary Data), 1.7.2.1 (UniProt), 1.7.99.1 (UniProt)
UniProt
Find proteins for P24474 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P24474  Go to UniProtKB:  P24474

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHE	G [auth A], L [auth B]	HEME D C34 H32 Fe N4 O10 XLQCGNUTSJTZNF-SOFPVUHFDM
HEC	F [auth A], K [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
PO4	C [auth A], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	D [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
OH	E [auth A], J [auth B]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.242 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.068	α = 90
b = 90.072	β = 90
c = 111.888	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
PROW	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-12-03 
Deposition Author(s): Nurizzo, D., Tegoni, M., Cambillau, C.

Revision History  

• Version 1.0: 1997-12-03
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance