SAXSdb — 8rfx

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

Copper-containing nitrite reductase

Bradyrhizobium sp. ORS 375

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 3 其他Polymer 3	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose × 3 COPPER (II) ION × 6 SULFATE ION × 27 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H0SLX7_BRAS3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–341； UniProt 25–364

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	8rfx
Deposition date deposition_date	2023-12-13
Structure title title	High pH (8.0) as-isolated MSOX movie series dataset 5 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [2.05 MGy]
Keywords keywords	Copper nitrite reductase, Copper-containing nitrite reductase, Br2DNiR, high pH, as-isolated, resting state, MSOX, 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.

8rfx__assembly_1__model_1

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

Download this curve (.dat)

8rfx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rfx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.64 Å
Rg (electron density)	28.38 Å
Total Rg	29.37 Å
Atom count	8185
Residues	1035
Excluded volume	144190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rfx__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 (6)

Entity 1 Entity 1 polymer

Description description	Copper-containing nitrite reductase
Molecular weight formula_weight	38144.0 kDa
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	3304

MDDLKLPRQRVDLVAPPFVHVHEQATKQGPKIMEFKLVVQEKKMVIDEKGTTFQAMTFNGSMPGPLMVVHEGDYVEVTLVNPATNTMPHNIDFHSATGALGGGALTLINPGEQVVLRWKATRTGVFVYHCAPGGPMIPWHVVSGMNGAVMVLPRDGLNDGHGHSLRYDRIYYIGEQDLYVPRDEKGNFKSYDSPGEAYSDTEEVMRKLTPTHVVFNGKAGALTGKNALNANVGENVLIVHSQANRDSRPHLIGGHGDYVWETGKFSNAPETGLETWFIRGGSAGAALYKFLQPGIYAYVTHNLIEAANLGATAHFKVEGKWNDDLMTQVKAPADIPTGSTNENLYFQG

Source Source

Source organism organism	Bradyrhizobium sp. ORS 375
NCBI taxonomy ID ncbi_taxonomy_id	566679
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 branched

Description description	beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	422

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Unit-cell length a length_a	107.210 Å
Unit-cell length b length_b	107.210 Å
Unit-cell length c length_c	107.210 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	1.400 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.1633
R_work r_work	0.1619
R_free r_free	0.1885

High pH (8.0) as-isolated MSOX movie series dataset 5 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [2.05 MGy]

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

8rfx__assembly_1__model_1

8rfx__assembly_1__model_1 | I(q)

8rfx__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

High pH (8.0) as-isolated MSOX movie series dataset 5 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [2.05 MGy]

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

8rfx__assembly_1__model_1

8rfx__assembly_1__model_1 | I(q)

8rfx__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)