SAXSdb — 4w9z

▼

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

Cytochrome c oxidase subunit 2

Bradyrhizobium diazoefficiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H7C6E5_BRADU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–139； UniProt 128–265

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4w9z
Deposition date deposition_date	2014-08-28
Structure title title	Crystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum
Keywords keywords	oxidoreductase, CuA, Respiration; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4w9z__assembly_1__model_1

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

Download this curve (.dat)

4w9z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4w9z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.43 Å
Rg (electron density)	14.18 Å
Total Rg	15.58 Å
Atom count	1093
Residues	138
Excluded volume	19726 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4w9z__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cytochrome c oxidase subunit 2
Molecular weight formula_weight	15598.0 kDa
EC 编号 ec_number	1.9.3.1
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	1378

MVPKADLTIKATGKQWYWSYAYPDNGKFEFDSLMAQDKQPRLLGVDNEMVVPVNKVIRVQVTGADVIHAFALPAFGVKIDAIPGRLNETWFKAAKTGMFYGQCSELCGKDHAFMPIAIRVVEDKEFASWVETAKKKFAS

Source Source

Source organism organism	Bradyrhizobium diazoefficiens
NCBI taxonomy ID ncbi_taxonomy_id	224911
Host organism host_organism	Escherichia coli BL21(DE3)

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	256

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4w9zA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

▶

Unit-cell length a length_a	32.431 Å
Unit-cell length b length_b	38.612 Å
Unit-cell length c length_c	59.644 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	59.120 Å
R factor r_factor	0.1102
R_work r_work	0.1089
R_free r_free	0.1336

Crystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum

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

Cytochrome c oxidase subunit 2

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

4w9z__assembly_1__model_1

4w9z__assembly_1__model_1 | I(q)

4w9z__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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum

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

Cytochrome c oxidase subunit 2

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

4w9z__assembly_1__model_1

4w9z__assembly_1__model_1 | I(q)

4w9z__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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)