← Back to search
1bjt

TOPOISOMERASE II RESIDUES 409-1201

Method: X-RAY DIFFRACTION Dmax: 119.8 Å Quality: GOOD
▼

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

TOPOISOMERASE II

Saccharomyces cerevisiae

UniProt P06786

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 409–1201 Fragment：DNA-BINDING AND CLEAVAGE CORE, RESIDUES 409-1201 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；pH 8.0 Resolution 2.50 Å R-free 0.269

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1BJT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BGW TOPOISOMERASE RESIDUES 410-1202, Deposited 1996-02-20 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 409–1201（793 aa） Fragment：RESIDUES 410 - 1202
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.277
1PVG Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II Deposited 2003-06-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–413（413 aa） Fragment：N-terminal ATPase region
Chain B 1–413（413 aa） Fragment：N-terminal ATPase region
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions microbatch under oil；pH 6.5；293 K；PEG 1500, Potassium Chloride, Glycerol, Sodium Cacodylate, pH 6.5, microbatch under oil, temperature 293K
Resolution 1.80 Å R-free 0.241
1QZR CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIAE TOPOISOMERASE II BOUND TO ICRF-187 (DEXRAZOXANE) Deposited 2003-09-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–413（413 aa） Fragment：N-terminal ATPase Region
Chain B 1–413（413 aa） Fragment：N-terminal ATPase Region
Not recorded MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 CDX (S)-4,4'-(1-METHYL-1,2-ETHANEDIYL)BIS-2,6-PIPERAZINEDIONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions microbatch under oil；pH 6.5；293 K；PEG 1500, POTASSIUM CHLORIDE, GLYCEROL, SODIUM CACODYLATE, pH 6.5, microbatch under oil, temperature 293K
Resolution 1.90 Å R-free 0.237
2RGR Topoisomerase IIA bound to G-segment DNA Deposited 2007-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 419–1177（759 aa） Fragment：DNA binding and cleavage domain (residues 419-1177)
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；12-20% PEG 1000, 100-250 mM MgCl2, 100 mM sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.278
3L4J Topoisomerase II-DNA cleavage complex, apo Deposited 2009-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric
Chain A 421–1177（757 aa） Fragment：RESIDUES 421-1177
Non-standard monomer：Yes (specific site not provided by mmCIF) TSP 3'-THIO-THYMIDINE-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；20% 1,4-BUTANEDIOL, 0.1M SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.48 Å R-free 0.259
3L4K Topoisomerase II-DNA cleavage complex, metal-bound Deposited 2009-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric
Chain A 421–1177（757 aa） Fragment：RESIDUES 421-1177
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 TSP 3'-THIO-THYMIDINE-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% 1,4-BUTANEDIOL, 0.1M SODIUM ACETATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.98 Å R-free 0.273
4GFH Topoisomerase II-DNA-AMPPNP complex Deposited 2012-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: decameric
Chain A 1–1177（1177 aa） Fragment：UNP RESIDUES 1-1177
Chain F 1–1177（1177 aa） Fragment：UNP RESIDUES 1-1177
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；23% PEG 300, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 4.41 Å R-free 0.275

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOP2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–793； UniProt 409–1201

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1bjt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bjt
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1bjt
Deposition date deposition_date1998-06-29
Structure title titleTOPOISOMERASE II RESIDUES 409-1201
Keywords keywordsTOPOISOMERASE, QUATERNARY CHANGE, DNA-BINDING, DNA TOPOLOGY; TOPOISOMERASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.06 Å
Radius of gyration Rg (electron density) rg_electron36.08 Å
Forward intensity I(0) i090689100.00
Molecular weight molecular_weight79262.0 kDa
Excluded volume excluded_volume100680 ų
Envelope volume envelope_volume141400 ų
Hydration-shell volume shell_volume35743 ų
Envelope diameter envelope_diameter123.1 Å
Shell Rg shell_rg38.47 Å
Envelope Rg envelope_rg35.86 Å
Shape Rg shape_rg36.02 Å
Total Rg total_rg36.49 Å
Total atoms total_atoms5598
Residues n_residues679
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax119.8 Å
Rg (real space) rg_real36.21 Å
Rg uncertainty (real space) rg_real_error1.17 Å
I(0) (real space) i0_real9.0690e+07
I(0) uncertainty (real space) i0_real_error1.5080e+06
Rg (reciprocal space) rg_reciprocal36.12 Å
I(0) (reciprocal space) i0_reciprocal90680000.0000
Solution quality estimate total_estimate0.8710
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.9 Å
Skewness Skewness skewness0.320
Kurtosis Kurtosis kurtosis-0.681
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12420000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.804; Smooth: 0.878
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1bjta_
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

CATH v4.4 (5 domains)

Domain ID domain_id1bjtA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id1bjtA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id1bjtA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase, domain 3
Domain ID domain_id1bjtA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily40 —
Domain ID domain_id1bjtA05
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily10 — Topoisomerase II, domain 5
▶

8. Citations (3)

▶

9. Files and Curves (10)