1zj9

Structure of Mycobacterium tuberculosis NirA protein

Method: X-RAY DIFFRACTION

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

Probable ferredoxin-dependent nitrite reductase NirA

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 IRON/SULFUR CLUSTER × 1 SIROHEME × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 IRON/SULFUR CLUSTER × 1 SIROHEME × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIR_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–566； UniProt 11–563 Author chain B； PDBConstruct 14–566； UniProt 11–563

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	1zj9
Deposition date deposition_date	2005-04-28
Structure title title	Structure of Mycobacterium tuberculosis NirA protein
Keywords keywords	NIRA, SULFITE, NITRITE, REDUCTASE, SIROHEME, FE4-S4, CYS-TYR COVALENT BOND, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1zj9__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1zj9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zj9__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	23.98 Å
Rg (electron density)	22.84 Å
Total Rg	23.54 Å
Atom count	4388
Residues	546
Excluded volume	77490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zj9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zj9__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Probable ferredoxin-dependent nitrite reductase NirA
Molecular weight formula_weight	63485.8 kDa
EC 编号 ec_number	1.7.7.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8792

MDVSHHHHHHGMATARPAKARNEGQWALGHREPLNANEELKKAGNPLDVRERIENIYAKQGFDSIDKTDLRGRFRWWGLYTQREQGYDGTWTGDDNIDKLEAKYFMMRVRCDGGALSAAALRTLGQISTEFARDTADISDRQNVQYHWIEVENVPEIWRRLDDVGLQTTEACGDCPRVVLGSPLAGESLDEVLDPTWAIEEIVRRYIGKPDFADLPRKYKTAISGLQDVAHEINDVAFIGVNHPEHGPGLDLWVGGGLSTNPMLAQRVGAWVPLGEVPEVWAAVTSVFRDYGYRRLRAKARLKFLIKDWGIAKFREVLETEYLKRPLIDGPAPEPVKHPIDHVGVQRLKNGLNAVGVAPIAGRVSGTILTAVADLMARAGSDRIRFTPYQKLVILDIPDALLDDLIAGLDALGLQSRPSHWRRNLMACSGIEFCKLSFAETRVRAQHLVPELERRLEDINSQLDVPITVNINGCPNSCARIQIADIGFKGQMIDDGHGGSVEGFQVHLGGHLGLDAGFGRKLRQHKVTSDELGDYIDRVVRNFVKHRSEGERFAQWVIRAEEDDLR

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SIROHEME
Molecular weight formula_weight	916.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1zj9a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.36 — Nitrite/Sulfite reductase N-terminal domain-like
Family Family family	d.58.36.1 — Duplicated SiR/NiR-like domains 1 and 3

Domain ID domain_id	d1zj9a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.36 — Nitrite/Sulfite reductase N-terminal domain-like
Family Family family	d.58.36.1 — Duplicated SiR/NiR-like domains 1 and 3

Domain ID domain_id	d1zj9a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.134 — Nitrite and sulphite reductase 4Fe-4S domain-like
Superfamily Superfamily superfamily	d.134.1 — Nitrite and sulphite reductase 4Fe-4S domain-like
Family Family family	d.134.1.1 — Nitrite and sulphite reductase 4Fe-4S domain-like

Domain ID domain_id	d1zj9a4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.134 — Nitrite and sulphite reductase 4Fe-4S domain-like
Superfamily Superfamily superfamily	d.134.1 — Nitrite and sulphite reductase 4Fe-4S domain-like
Family Family family	d.134.1.1 — Nitrite and sulphite reductase 4Fe-4S domain-like

Domain ID domain_id	d1zj9b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.36 — Nitrite/Sulfite reductase N-terminal domain-like
Family Family family	d.58.36.1 — Duplicated SiR/NiR-like domains 1 and 3

Domain ID domain_id	d1zj9b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.36 — Nitrite/Sulfite reductase N-terminal domain-like
Family Family family	d.58.36.1 — Duplicated SiR/NiR-like domains 1 and 3

Domain ID domain_id	d1zj9b3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.134 — Nitrite and sulphite reductase 4Fe-4S domain-like
Superfamily Superfamily superfamily	d.134.1 — Nitrite and sulphite reductase 4Fe-4S domain-like
Family Family family	d.134.1.1 — Nitrite and sulphite reductase 4Fe-4S domain-like

Domain ID domain_id	d1zj9b4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.134 — Nitrite and sulphite reductase 4Fe-4S domain-like
Superfamily Superfamily superfamily	d.134.1 — Nitrite and sulphite reductase 4Fe-4S domain-like
Family Family family	d.134.1.1 — Nitrite and sulphite reductase 4Fe-4S domain-like

CATH v4.4 (6 domains)

Domain ID domain_id	1zj9A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	480 — Sulfite Reductase Hemoprotein; domain 2
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein;Domain 2

Domain ID domain_id	1zj9A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	1zj9A04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	1zj9B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	480 — Sulfite Reductase Hemoprotein; domain 2
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein;Domain 2

Domain ID domain_id	1zj9B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	1zj9B04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

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Unit-cell length a length_a	59.983 Å
Unit-cell length b length_b	83.307 Å
Unit-cell length c length_c	108.801 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	55.000 Å
R factor r_factor	0.2061
R_work r_work	0.2019
R_free r_free	0.2800

Structure of Mycobacterium tuberculosis NirA protein

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

Probable ferredoxin-dependent nitrite reductase NirA

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1zj9__assembly_1__model_1

1zj9__assembly_1__model_1 | I(q)

1zj9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of Mycobacterium tuberculosis NirA protein

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

Probable ferredoxin-dependent nitrite reductase NirA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1zj9__assembly_1__model_1

1zj9__assembly_1__model_1 | I(q)

1zj9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)