SAXSdb — 4ely

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

DNA gyrase subunit A

Shigella flexneri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CcdB × 2 （Q84B82） SULFATE ION × 1 CHLORIDE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GYRA_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–156； UniProt 363–497 Author chain B； PDBConstruct 22–156； UniProt 363–497

CcdB

Aliivibrio fischeri

UniProt Q84B82

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 （P0AES5） SULFATE ION × 1 CHLORIDE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q84B82_VIBFI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–105； UniProt 1–105 Author chain D； PDBConstruct 1–105； UniProt 1–105

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	4ely
Deposition date deposition_date	2012-04-11
Structure title title	CCDBVFI:GYRA14EC
Keywords keywords	ALPHA+BETA, TOPOISOMERASE, TOXIN-ISOMERASE complex; TOXIN/ISOMERASE
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.

4ely__assembly_1__model_1

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

Download this curve (.dat)

4ely__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ely__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.52 Å
Rg (electron density)	23.13 Å
Total Rg	23.95 Å
Atom count	3612
Residues	466
Excluded volume	64788 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ely__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 (5)

Entity 1 Entity 1 polymer

Description description	DNA gyrase subunit A
Molecular weight formula_weight	17567.0 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	3906

MGSSHHHHHHSSGLVPRGSHMTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADR

Source Source

Source organism organism	Shigella flexneri
NCBI taxonomy ID ncbi_taxonomy_id	623
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CcdB
Molecular weight formula_weight	11879.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSQFTLYKNKDKSSAKTYPYFVDVQSDLLDNLNTRLVIPLTPIELLDKKAPSHLCPTIHIDEGDFIMLTQQMTSVPVKILSEPVNELSTFRNEIIAAIDFLITGI

Source Source

Source organism organism	Aliivibrio fischeri
NCBI taxonomy ID ncbi_taxonomy_id	668
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	256

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4elya_
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	d4elyb_
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	d4elyc_
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	d4elyd_
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	4elyA00
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	4elyB00
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	4elyC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	4elyD00
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	130.073 Å
Unit-cell length b length_b	90.833 Å
Unit-cell length c length_c	58.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.932 Å
Low-resolution limit resolution_low	24.624 Å
R factor r_factor	0.1871
R_work r_work	0.1855
R_free r_free	0.2167

CCDBVFI:GYRA14EC

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

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

4ely__assembly_1__model_1

4ely__assembly_1__model_1 | I(q)

4ely__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CCDBVFI:GYRA14EC

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

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

4ely__assembly_1__model_1

4ely__assembly_1__model_1 | I(q)

4ely__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)