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5j5q

AMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II

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

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 Homooligomer Protein 2 DNA 2 ;DNA (5'-D(*GP*CP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*GP*C)-3') ; × 2 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 2 Consistent with all polymers
2 Protein homooligomer Homooligomer Protein 2 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 Consistent with protein count

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 1
Chains and sequence ranges Author chain A； PDBConstruct 2–403； UniProt 1–402 Author chain B； PDBConstruct 2–403； UniProt 1–402 Author chain C； PDBConstruct 2–403； UniProt 1–402 Author chain D； PDBConstruct 2–403； UniProt 1–402

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_id5j5q
Deposition date deposition_date2016-04-03
Structure title titleAMP-PNP-stabilized ATPase domain of topoisomerase IV from Streptococcus pneumoniae, complex type II
Keywords keywordsStreptococcus PNEUMONIAE, TOPOISOMERASE IV, DNA BINDING, ISOMERASE-DNA COMPLEX, ATPase domain, T-segment; 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.

5j5q__assembly_2__model_1

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

Download this curve (.dat)

5j5q__assembly_2__model_1 | I(q)

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

5j5q__assembly_2__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）29.06 Å
Rg (electron density)27.97 Å
Total Rg28.61 Å
Atom count5564
Residues789
Excluded volume96644 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5j5q__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5j5q__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 (4)

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id5j5qA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id5j5qA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5j5qB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id5j5qB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5j5qC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id5j5qC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5j5qD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id5j5qD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10 —
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7. Citations (1)