2zbk

Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms

Method: X-RAY DIFFRACTION

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

Type II DNA topoisomerase VI subunit A

Sulfolobus shibatae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Type 2 DNA topoisomerase 6 subunit B × 2 （O05207） RADICICOL × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Type 2 DNA topoisomerase 6 subunit B × 2 （O05207） RADICICOL × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOP6A_SULSH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–389； UniProt 1–389 Author chain C； PDBConstruct 1–389； UniProt 1–389 Author chain E； PDBConstruct 1–389； UniProt 1–389 Author chain G； PDBConstruct 1–389； UniProt 1–389

Type 2 DNA topoisomerase 6 subunit B

Sulfolobus shibatae

UniProt O05207

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Type II DNA topoisomerase VI subunit A × 2 （O05208） RADICICOL × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Type II DNA topoisomerase VI subunit A × 2 （O05208） RADICICOL × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOP6B_SULSH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–530； UniProt 1–530 Author chain D； PDBConstruct 1–530； UniProt 1–530 Author chain F； PDBConstruct 1–530； UniProt 1–530 Author chain H； PDBConstruct 1–530； UniProt 1–530

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	2zbk
Deposition date deposition_date	2007-10-22
Structure title title	Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms
Keywords keywords	;DNA topoisomerase, DNA binding protein, decatenation, ATPase, drug design, DNA-binding, Magnesium, Metal-binding, ATP-binding, Nucleotide-binding, Structural Genomics, Paris-Sud Yeast Structural Genomics, YSG, 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.

2zbk__assembly_1__model_1

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

Download this curve (.dat)

2zbk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zbk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	63.88 Å
Rg (electron density)	63.71 Å
Total Rg	63.81 Å
Atom count	13888
Residues	1706
Excluded volume	250240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zbk__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zbk__assembly_2__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	Type II DNA topoisomerase VI subunit A
Molecular weight formula_weight	45122.0 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,C,E,G
Atom count atom_count	27776

MSSEFISKVDKEARRKAANILRDKFLNLVEQLKKGEPLVMEIPMRTLSNAIYDEKRKLLLLGEKKLRRNFLDLNEAKRFMQTVLMASIIYDALVSDEYPTIRDLYYRGKHSLLLKSIEGNKIVSEENTWDEQKESDSVIVDIEVFTSLLREEMLILSKEKGKVVGNLRIRSGNDVIDLSKTGHGAYAIEPTPDLIDFIDVDAEFVLVVEKDAVFQQLHRAGFWKQYKSILITSAGQPDRATRRFVRRLNEELKLPVYILTDADPYGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDIFGNSRKKPYLSEAERKNYIIKAKDADIKRAEEIKNYEWFKTKAWQEEINTFLQRKAKLEIEAMASKGLKFLAFQYIPEKITNKDYIA

Source Source

Source organism organism	Sulfolobus shibatae
Common name common_name	archaea
NCBI taxonomy ID ncbi_taxonomy_id	2286
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Type 2 DNA topoisomerase 6 subunit B
Molecular weight formula_weight	60614.6 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	B,D,F,H

MSAKEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVTYYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKDEDFRSPSADSLSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIPVGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKESIAEVENIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLLAYLKYIPEVSRSLATFLASGNKELVSKYQNEISEGLFKLISKKLDLINIEEYRKVYRVDSE

Source Source

Source organism organism	Sulfolobus shibatae
Common name common_name	archaea
NCBI taxonomy ID ncbi_taxonomy_id	2286
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	RADICICOL
Molecular weight formula_weight	364.8 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id	2zbkA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2zbkA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2zbkB01
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	2zbkB02
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	2zbkB03
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	2zbkC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2zbkC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2zbkD01
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	2zbkD02
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	2zbkD03
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	2zbkE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2zbkE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2zbkF01
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	2zbkF02
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	2zbkF03
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	2zbkG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2zbkG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2zbkH01
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	2zbkH02
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	2zbkH03
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	114.960 Å
Unit-cell length b length_b	200.530 Å
Unit-cell length c length_c	329.070 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.560 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.3130
R_work r_work	0.3120
R_free r_free	0.3330

Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms

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

Type II DNA topoisomerase VI subunit A

State in the Current Structure

Other States of the Same Protein in the Database

Type 2 DNA topoisomerase 6 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

2zbk__assembly_1__model_1

2zbk__assembly_1__model_1 | I(q)

2zbk__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 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

7. Citations (1)

Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms

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

Type II DNA topoisomerase VI 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

Type 2 DNA topoisomerase 6 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

2zbk__assembly_1__model_1

2zbk__assembly_1__model_1 | I(q)

2zbk__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 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

7. Citations (1)