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2rgr

Topoisomerase IIA bound to G-segment DNA

Method: X-RAY DIFFRACTION Dmax: 112.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA topoisomerase 2

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–DNA Homooligomer Protein × 2 DNA 4 PDB declaration: hexameric（6） Consistent with all polymer counts Chain A； UniProt 419–1177 Fragment：DNA binding and cleavage domain (residues 419-1177) DNA × 2 DNA × 2 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

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 2RGR 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 oligomeric state Different ligand/ion 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
1BJT TOPOISOMERASE II RESIDUES 409-1201 Deposited 1998-06-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 409–1201（793 aa） Fragment：DNA-BINDING AND CLEAVAGE CORE, RESIDUES 409-1201
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.50 Å R-free 0.269
1PVG Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II Deposited 2003-06-27 Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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
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 3
Chains and sequence ranges Author chain A； PDBConstruct 1–759； UniProt 419–1177

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 2rgr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2rgr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2rgr
Deposition date deposition_date2007-10-04
Structure title titleTopoisomerase IIA bound to G-segment DNA
Keywords keywords;protein-DNA complex, ATP-binding, DNA-binding, Isomerase, Nucleotide-binding, Nucleus, Phosphoprotein, Topoisomerase, Isomerase-DNA COMPLEX ;; Isomerase/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.85 Å
Radius of gyration Rg (electron density) rg_electron33.00 Å
Forward intensity I(0) i0151221000.00
Molecular weight molecular_weight94389.0 kDa
Excluded volume excluded_volume116510 ų
Envelope volume envelope_volume158730 ų
Hydration-shell volume shell_volume41439 ų
Envelope diameter envelope_diameter121.2 Å
Shell Rg shell_rg38.39 Å
Envelope Rg envelope_rg33.40 Å
Shape Rg shape_rg32.97 Å
Total Rg total_rg33.52 Å
Total atoms total_atoms6620
Residues n_residues755
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.6 Å
Rg (real space) rg_real32.99 Å
Rg uncertainty (real space) rg_real_error0.94 Å
I(0) (real space) i0_real1.5120e+08
I(0) uncertainty (real space) i0_real_error2.2850e+06
Rg (reciprocal space) rg_reciprocal32.93 Å
I(0) (reciprocal space) i0_reciprocal151200000.0000
Solution quality estimate total_estimate0.8627
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.2 Å
Skewness Skewness skewness0.491
Kurtosis Kurtosis kurtosis-0.091
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21060000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.841
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2rgra_
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_id2rgrA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily670 —
Domain ID domain_id2rgrA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id2rgrA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily10 — Topoisomerase II, domain 5
Domain ID domain_id2rgrA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily40 —
Domain ID domain_id2rgrA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase, domain 3
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8. Citations (1)

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9. Files and Curves (10)