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3ksb

Detailed structural insight into the DNA cleavage complex of type IIA topoisomerases (re-sealed form)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA topoisomerase 4 subunit A

Streptococcus pneumoniae

UniProt P72525

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 4 DNA 2 DNA topoisomerase 4 subunit B × 2 （Q59961） 5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*TP*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3' × 1 5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*TP*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3' × 1 MAGNESIUM ION × 2 water × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
2nov 2nov

2 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3foe 3fof 3k9f 3ksa 3ksb 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe

18 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PARC_STRPN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–488； UniProt 1–488 Author chain B； PDBConstruct 1–488； UniProt 1–488

DNA topoisomerase 4 subunit B

Streptococcus pneumoniae

UniProt Q59961

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 4 DNA 2 DNA topoisomerase 4 subunit A × 2 （P72525） 5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*TP*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3' × 1 5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*TP*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3' × 1 MAGNESIUM ION × 2 water × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
5j5q

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3foe 3fof 3k9f 3ksa 3ksb 3ltn 3rad 3rae 3raf 4juo 4koe 4kpe

19 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PARE_STRPN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 25–268； UniProt 404–647 Author chain D； PDBConstruct 25–268； UniProt 404–647

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_id3ksb
Deposition date deposition_date2009-11-21
Structure title titleDetailed structural insight into the DNA cleavage complex of type IIA topoisomerases (re-sealed form)
Keywords keywords;Topoisomerase, protein-DNA cleavage complex, Streptococcus pneumoniae, DNA-binding, nucleotide-binding, quinolone, Sealed DNA form, ISOMERASE-DNA COMPLEX ;; ISOMERASE/DNA
Experimental Method methodX-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.

3ksb__assembly_1__model_1

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

Download this curve (.dat)

3ksb__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3ksb__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）35.68 Å
Rg (electron density)35.70 Å
Total Rg36.06 Å
Atom count10597
Residues1409
Excluded volume185850 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3ksb__assembly_1__model_1 hexameric （6） 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 (6)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3ksba_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.11 — Type II DNA topoisomerase C-terminal domain-like
Superfamily Superfamily superfamilye.11.1 — Type II DNA topoisomerase C-terminal domain-like
Family Family familye.11.1.1 — Type II DNA topoisomerase C-terminal domain-like
Domain ID domain_idd3ksbb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.11 — Type II DNA topoisomerase C-terminal domain-like
Superfamily Superfamily superfamilye.11.1 — Type II DNA topoisomerase C-terminal domain-like
Family Family familye.11.1.1 — Type II DNA topoisomerase C-terminal domain-like
Domain ID domain_idd3ksbc_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.78 — DNA gyrase B, C-terminal domain-like
Superfamily Superfamily superfamilye.78.1 — DNA gyrase B, C-terminal domain-like
Family Family familye.78.1.1 — DNA gyrase B, C-terminal domain
Domain ID domain_idd3ksbd_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.78 — DNA gyrase B, C-terminal domain-like
Superfamily Superfamily superfamilye.78.1 — DNA gyrase B, C-terminal domain-like
Family Family familye.78.1.1 — DNA gyrase B, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id3ksbC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id3ksbD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
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7. Citations (2)