4ckk

Apo structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit

Method: X-RAY DIFFRACTION

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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 homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	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 1–493； UniProt 30–522 Author chain B； PDBConstruct 1–493； UniProt 30–522 Author chain C； PDBConstruct 1–493； UniProt 30–522 Author chain D； PDBConstruct 1–493； UniProt 30–522

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	4ckk
Deposition date deposition_date	2014-01-07
Structure title title	Apo structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit
Keywords keywords	ISOMERASE, DNA GYRASE, TOPOISOMERASE, ANTIBIOTIC TARGET; 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.

4ckk__assembly_1__model_1

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

Download this curve (.dat)

4ckk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ckk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.31 Å
Rg (electron density)	37.84 Å
Total Rg	38.11 Å
Atom count	7482
Residues	969
Excluded volume	133300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ckk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ckk__assembly_2__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	DNA GYRASE SUBUNIT A
Molecular weight formula_weight	55381.4 kDa
EC 编号 ec_number	5.99.1.3
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	16106

VGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEIT

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1056

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ckka_
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	d4ckkb_
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	d4ckkc_
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	d4ckkd_
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

CATH v4.4 (9 domains)

Domain ID domain_id	4ckkA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily	10 — Topoisomerase II, domain 5

Domain ID domain_id	4ckkA03
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	4ckkB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily	10 — Topoisomerase II, domain 5

Domain ID domain_id	4ckkB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4ckkB03
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	4ckkC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily	10 — Topoisomerase II, domain 5

Domain ID domain_id	4ckkC03
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	4ckkD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily	10 — Topoisomerase II, domain 5

Domain ID domain_id	4ckkD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily	10 — Topoisomerase, domain 3

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Unit-cell length a length_a	93.570 Å
Unit-cell length b length_b	95.530 Å
Unit-cell length c length_c	95.890 Å
Unit-cell angle α angle_alpha	105.16 °
Unit-cell angle β angle_beta	118.81 °
Unit-cell angle γ angle_gamma	103.42 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	81.510 Å
R factor r_factor	0.1703
R_work r_work	0.1694
R_free r_free	0.1886

Apo structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ckk__assembly_1__model_1

4ckk__assembly_1__model_1 | I(q)

4ckk__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (4 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Apo structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ckk__assembly_1__model_1

4ckk__assembly_1__model_1 | I(q)

4ckk__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (4 domains)

CATH v4.4 (9 domains)

7. Citations (1)