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.

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

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

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(by identity cutoff) | 3D Structure

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
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24474
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DHE Query on DHE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B]	G [auth A], L [auth B]	HEME D C₃₄ H₃₂ Fe N₄ O₁₀ XLQCGNUTSJTZNF-YDXXJHAFSA-L		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B]	F [auth A], K [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B]	D [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
OH Query on OH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B]	E [auth A], J [auth B]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 1997-12-03

Deposition Author(s):

Nurizzo, D.

Tegoni, M.

Cambillau, C.

Revision History (Full details and data files)

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
Version 1.3: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

1NIR

OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)