SAXSdb — 1x75

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

DNA gyrase subunit A

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cytotoxic protein ccdB × 2 （P62555） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GYRA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–132； UniProt 363–494 Author chain B； PDBConstruct 1–132； UniProt 363–494

Cytotoxic protein ccdB

Escherichia coli

UniProt P62555

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA gyrase subunit A × 2 （P09097） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCDB_ECO57
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–101； UniProt 1–101 Author chain D； PDBConstruct 1–101； UniProt 1–101

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	1x75
Deposition date deposition_date	2004-08-13
Structure title title	CcdB:GyrA14 complex
Keywords keywords	gyrase, CcdB, topoisomerase, plasmid addiction, TA system, bacterial cell death, ISOMERASE-SIGNALING PROTEIN COMPLEX; ISOMERASE/SIGNALING PROTEIN
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.

1x75__assembly_1__model_1

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

Download this curve (.dat)

1x75__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1x75__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.51 Å
Rg (electron density)	22.38 Å
Total Rg	23.20 Å
Atom count	3415
Residues	451
Excluded volume	61141 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1x75__assembly_1__model_1`	tetrameric （4）	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	DNA gyrase subunit A
Molecular weight formula_weight	14921.1 kDa
EC 编号 ec_number	5.99.1.3
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	3484

TRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGS

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cytotoxic protein ccdB
Molecular weight formula_weight	11721.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1x75a1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.11 — Type II DNA topoisomerase C-terminal domain-like
Superfamily Superfamily superfamily	e.11.1 — Type II DNA topoisomerase C-terminal domain-like
Family Family family	e.11.1.1 — Type II DNA topoisomerase C-terminal domain-like

Domain ID domain_id	d1x75b_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.11 — Type II DNA topoisomerase C-terminal domain-like
Superfamily Superfamily superfamily	e.11.1 — Type II DNA topoisomerase C-terminal domain-like
Family Family family	e.11.1.1 — Type II DNA topoisomerase C-terminal domain-like

Domain ID domain_id	d1x75c_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.6 — Cell growth inhibitor/plasmid maintenance toxic component
Family Family family	b.34.6.1 — CcdB

Domain ID domain_id	d1x75d_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.6 — Cell growth inhibitor/plasmid maintenance toxic component
Family Family family	b.34.6.1 — CcdB

CATH v4.4 (4 domains)

Domain ID domain_id	1x75A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily	10 — Topoisomerase, domain 3

Domain ID domain_id	1x75B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily	10 — Topoisomerase, domain 3

Domain ID domain_id	1x75C00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1x75D00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	110 —

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Unit-cell length a length_a	52.124 Å
Unit-cell length b length_b	83.344 Å
Unit-cell length c length_c	110.919 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2299
R_work r_work	0.2239
R_free r_free	0.2979

CcdB:GyrA14 complex

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

DNA gyrase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Cytotoxic protein ccdB

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

1x75__assembly_1__model_1

1x75__assembly_1__model_1 | I(q)

1x75__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CcdB:GyrA14 complex

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

DNA gyrase subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytotoxic protein ccdB

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

1x75__assembly_1__model_1

1x75__assembly_1__model_1 | I(q)

1x75__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)