SAXSdb — 1nir

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NITRITE REDUCTASE

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 26–568 Chain B； UniProt 26–568	Not recorded	PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 2 OH HYDROXIDE ION × 2 HEC HEME C × 2 DHE HEME D × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.4；PROTEIN WAS CRYSTALLIZED FROM @M NA/K2 PHOSPHATE, 50MM TRIS-HCL, PH 8.4	Resolution 2.15 Å R-free 0.242

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1NIR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BL9 CONFORMATIONAL CHANGES OCCURRING UPON REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa） Chain B 26–568（543 aa）	Not recorded	HEC HEME C × 2 DHE HEME D × 2 OH HYDROXIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2	Resolution 2.90 Å R-free 0.233
1GJQ Pseudomonas aeruginosa cd1 nitrite reductase reduced cyanide complex Deposited 2001-08-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa） Chain B 26–568（543 aa）	Not recorded	HEC HEME C × 2 DHE HEME D × 2 CYN CYANIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；2M NA/K2 PHOSPHATE, 50MM TRIS-HCL, PH 8.4	Resolution 2.70 Å R-free 0.247
1HZU DOMAIN SWING UPON HIS TO ALA MUTATION IN NITRITE REDUCTASE OF PSEUDOMONAS AERUGINOSA Deposited 2001-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa）	Mutation：H327A	HEC HEME C × 2 DHE HEME D × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；PEG 5000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.248
1HZV DOMAIN SWING UPON HIS TO ALA MUTATION IN NITRITE REDUCTASE OF PSEUDOMONAS AERUGINOSA Deposited 2001-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa）	Mutation：H369A	HEC HEME C × 2 DHE HEME D × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.83 Å R-free 0.296
1N15 FOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa） Chain B 26–568（543 aa）	Not recorded	HEC HEME C × 2 DHE HEME D × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2	Resolution 2.90 Å R-free 0.247
1N50 FOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa） Chain B 26–568（543 aa）	Not recorded	HEC HEME C × 2 DHE HEME D × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2	Resolution 2.90 Å R-free 0.246
1N90 FOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa） Chain B 26–568（543 aa）	Not recorded	HEC HEME C × 2 DHE HEME D × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2	Resolution 2.90 Å R-free 0.241
1NNO CONFORMATIONAL CHANGES OCCURRING UPON NO BINDING IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA Deposited 1998-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa） Chain B 26–568（543 aa）	Not recorded	HEC HEME C × 2 DHE HEME D × 2 NO NITRIC OXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2	Resolution 2.65 Å R-free 0.243
5GUW Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa Deposited 2016-08-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain M 1–568（568 aa） Fragment：cd1 nitrite reductase Chain N 1–568（568 aa） Fragment：cd1 nitrite reductase	Not recorded	HEC HEME C × 2 DHE HEME D × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, 0.2M CsCl, 12% PEG3350	Resolution 3.20 Å R-free 0.254
6TPO Conformation of cd1 nitrite reductase NirS without bound heme d1 Deposited 2019-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 2 BU3 (R,R)-2,3-BUTANEDIOL × 2 HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.1M Phosphate/citrate pH4.2 40% (v/v) PEG300	Resolution 1.86 Å R-free 0.194
6TSI cd1 nitrite reductase NirS with bound dihydro-heme d1 Deposited 2019-12-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–568（543 aa） Chain B 26–568（543 aa）	Not recorded	HEC HEME C × 2 DHE HEME D × 2 PO4 PHOSPHATE ION × 5 CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.9M K2HPO4 0.1M Tris-HCl pH 8	Resolution 2.38 Å R-free 0.280

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NIRS_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–543； UniProt 26–568 Author chain B； PDBConstruct 1–543； UniProt 26–568

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1nir
Deposition date deposition_date	1997-06-17
Structure title title	OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA
Keywords keywords	NITRITE REDUCTASE, PSEUDOMONAS AERUGINOSA, HEMOPROTEIN, DENITRIFICATION, DOMAIN SWAPPING; NITRITE REDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.13 Å
Radius of gyration Rg (electron density) rg_electron	32.69 Å
Forward intensity I(0) i0	230135000.00
Molecular weight molecular_weight	122170.0 kDa
Excluded volume excluded_volume	152890 Å³
Envelope volume envelope_volume	183030 Å³
Hydration-shell volume shell_volume	46199 Å³
Envelope diameter envelope_diameter	113.0 Å
Shell Rg shell_rg	39.84 Å
Envelope Rg envelope_rg	32.80 Å
Shape Rg shape_rg	32.68 Å
Total Rg total_rg	33.22 Å
Total atoms total_atoms	8613
Residues n_residues	1077
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	109.4 Å
Rg (real space) rg_real	33.14 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	2.3010e+08
I(0) uncertainty (real space) i0_real_error	3.8050e+06
Rg (reciprocal space) rg_reciprocal	33.14 Å
I(0) (reciprocal space) i0_reciprocal	230100000.0000
Solution quality estimate total_estimate	0.8863
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.5 Å
Skewness Skewness skewness	0.352
Kurtosis Kurtosis kurtosis	-0.417
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	73020000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.914

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	NITRITE REDUCTASE
Molecular weight formula_weight	60259.1 kDa
EC 编号 ec_number	1.9.3.2
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9483

KDDMKAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	HYDROXIDE ION
Molecular weight formula_weight	17.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	HEME D
Molecular weight formula_weight	712.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	870

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1nira1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.2 — N-terminal (heme c) domain of cytochrome cd1-nitrite reductase

Domain ID domain_id	d1nira2
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.2 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
Family Family family	b.70.2.1 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

Domain ID domain_id	d1nirb1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.2 — N-terminal (heme c) domain of cytochrome cd1-nitrite reductase

Domain ID domain_id	d1nirb2
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.2 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
Family Family family	b.70.2.1 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

CATH v4.4 (4 domains)

Domain ID domain_id	1nirA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1nirA02
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	20 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

Domain ID domain_id	1nirB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1nirB02
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	20 — C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase

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8. Citations (1)

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Unit-cell length a length_a	163.068 Å
Unit-cell length b length_b	90.072 Å
Unit-cell length c length_c	111.888 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2420

fit	/app/data/saxs_computation/ni/1nir/1nir.fit
pddf	/app/data/pr_computation/ni/1nir/1nir.pr.out
profile	/app/data/saxs_computation/ni/1nir/1nir.dat

OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA