1mx0

Structure of topoisomerase subunit

Method: X-RAY DIFFRACTION

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

Type II DNA topoisomerase VI subunit B

Sulfolobus shibatae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 SODIUM ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TP6B_SULSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–472； UniProt 1–470 Author chain B； PDBConstruct 3–472； UniProt 1–470 Author chain C； PDBConstruct 3–472； UniProt 1–470 Author chain D； PDBConstruct 3–472； UniProt 1–470 Author chain E； PDBConstruct 3–472； UniProt 1–470 Author chain F； PDBConstruct 3–472； UniProt 1–470

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	1mx0
Deposition date deposition_date	2002-10-01
Structure title title	Structure of topoisomerase subunit
Keywords keywords	GHKL ATPase, topoisomerase, ISOMERASE; 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.

1mx0__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1mx0__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mx0__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.75 Å
Rg (electron density)	28.69 Å
Total Rg	29.48 Å
Atom count	7490
Residues	917
Excluded volume	134580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mx0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1mx0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1mx0__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	Type II DNA topoisomerase VI subunit B
Molecular weight formula_weight	54004.2 kDa
EC 编号 ec_number	5.99.1.3
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	23057

GAMSAKEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKYEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVEDIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLLA

Source Source

Source organism organism	Sulfolobus shibatae
NCBI taxonomy ID ncbi_taxonomy_id	2286
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	811

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d1mx0a1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.3 — Topoisomerase VI-B subunit middle domain

Domain ID domain_id	d1mx0a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1mx0a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

Domain ID domain_id	d1mx0b1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.3 — Topoisomerase VI-B subunit middle domain

Domain ID domain_id	d1mx0b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1mx0b3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

Domain ID domain_id	d1mx0c1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.3 — Topoisomerase VI-B subunit middle domain

Domain ID domain_id	d1mx0c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1mx0c3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

Domain ID domain_id	d1mx0d1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.3 — Topoisomerase VI-B subunit middle domain

Domain ID domain_id	d1mx0d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1mx0d3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

Domain ID domain_id	d1mx0e1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.3 — Topoisomerase VI-B subunit middle domain

Domain ID domain_id	d1mx0e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1mx0e3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

Domain ID domain_id	d1mx0f1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.3 — Topoisomerase VI-B subunit middle domain

Domain ID domain_id	d1mx0f2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1mx0f3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

CATH v4.4 (18 domains)

Domain ID domain_id	1mx0A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	1mx0A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1mx0A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1mx0B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	1mx0B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1mx0B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1mx0C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	1mx0C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1mx0C03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1mx0D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	1mx0D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1mx0D03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1mx0E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	1mx0E02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1mx0E03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1mx0F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily	10 — Histidine kinase-like ATPase, C-terminal domain

Domain ID domain_id	1mx0F02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1mx0F03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	146.655 Å
Unit-cell length b length_b	219.192 Å
Unit-cell length c length_c	106.921 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	24

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2185
R_work r_work	0.2145
R_free r_free	0.2633

Structure of topoisomerase subunit

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

Type II DNA topoisomerase VI subunit B

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

1mx0__assembly_2__model_1

1mx0__assembly_2__model_1 | I(q)

1mx0__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

CATH v4.4 (18 domains)

7. Citations (1)

Structure of topoisomerase subunit

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

Type II DNA topoisomerase VI subunit B

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

1mx0__assembly_2__model_1

1mx0__assembly_2__model_1 | I(q)

1mx0__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

CATH v4.4 (18 domains)

7. Citations (1)