SAXSdb — 9hs0

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

Copper-containing nitrite reductase

Bradyrhizobium diazoefficiens USDA 110

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	COPPER (II) ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q89EJ6_BRADU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–367； UniProt 1–367

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	9hs0
Deposition date deposition_date	2024-12-18
Last revision last_revision	2025-06-11
Structure title title	Copper-containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110
Keywords keywords	Copper-binding protein, Reductase, NirK, 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.

9hs0__assembly_1__model_1

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

Download this curve (.dat)

9hs0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9hs0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.91 Å
Rg (electron density)	27.96 Å
Total Rg	28.87 Å
Atom count	7680
Residues	1005
Excluded volume	136630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9hs0__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Copper-containing nitrite reductase
Molecular weight formula_weight	39758.4 kDa
EC 编号 ec_number	1.7.2.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3339

MLPMFTRRAALISAAATALMLATPALAADDLKLPRQKVELVAPPFVHAHEQATKQGPKIVEFKLTIEEKKVVIDEKGTTFQAMTFNGSMPGPLMVVHEGDYVETTLVNPATNTMPHNIDFHSATGALGGGALTLINPGEQVVLRWKATKTGVFVYHCAPGGPMIPWHVVSGMNGAVMVLPRDGLNDGKGHALKYDKVYYVGEQDMYVPRDEKGNFKSYDSPGEAFTDTEEMMKKLIPSHVVFNGKVGALTGKNALTANVGENVLIVHSQANRDSRPHLIGGHGDYVWETGKFGNAPEVGLETWFIRGGSAGAAMYKFMQPGIYAYVTHNLIEAADLGATAHFKVEGKWNDDLMTQVKAPAEIPANTN

Source Source

Source organism organism	Bradyrhizobium diazoefficiens USDA 110
NCBI taxonomy ID ncbi_taxonomy_id	224911
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	572

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Unit-cell length a length_a	105.808 Å
Unit-cell length b length_b	105.808 Å
Unit-cell length c length_c	105.808 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	12

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	35.270 Å
R factor r_factor	0.0911
R_work r_work	0.0902
R_free r_free	0.1090

Copper-containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110

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

Copper-containing nitrite reductase

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

9hs0__assembly_1__model_1

9hs0__assembly_1__model_1 | I(q)

9hs0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Copper-containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110

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

Copper-containing nitrite reductase

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

9hs0__assembly_1__model_1

9hs0__assembly_1__model_1 | I(q)

9hs0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)