SAXSdb — 1pvg

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

DNA topoisomerase II

Saccharomyces cerevisiae

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 1–413 Chain B； UniProt 1–413	Fragment：N-terminal ATPase region 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

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 1PVG	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 mutation/modification 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 mutation/modification 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
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 mutation/modification 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 oligomeric state 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 6–418； UniProt 1–413 Author chain B； PDBConstruct 6–418； UniProt 1–413

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	1pvg
Deposition date deposition_date	2003-06-27
Structure title title	Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II
Keywords keywords	GHKL ATPase domain, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	27.93 Å
Radius of gyration Rg (electron density) rg_electron	27.15 Å
Forward intensity I(0) i0	128253000.00
Molecular weight molecular_weight	88471.0 kDa
Excluded volume excluded_volume	110100 Å³
Envelope volume envelope_volume	131730 Å³
Hydration-shell volume shell_volume	39064 Å³
Envelope diameter envelope_diameter	90.8 Å
Shell Rg shell_rg	35.80 Å
Envelope Rg envelope_rg	27.23 Å
Shape Rg shape_rg	27.16 Å
Total Rg total_rg	27.94 Å
Total atoms total_atoms	6147
Residues n_residues	736
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	84.5 Å
Rg (real space) rg_real	27.77 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.2830e+08
I(0) uncertainty (real space) i0_real_error	1.8320e+06
Rg (reciprocal space) rg_reciprocal	27.82 Å
I(0) (reciprocal space) i0_reciprocal	128300000.0000
Solution quality estimate total_estimate	0.9066
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.1 Å
Skewness Skewness skewness	0.177
Kurtosis Kurtosis kurtosis	-0.498
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30220000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA topoisomerase II
Molecular weight formula_weight	48567.9 kDa
EC 编号 ec_number	5.99.1.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6892

GHMVTMSTEPVSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIADANEENALK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	745

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1pvga1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1pvga2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

Domain ID domain_id	d1pvgb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.3 — DNA gyrase/MutL, second domain

Domain ID domain_id	d1pvgb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamily	d.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family family	d.122.1.2 — DNA gyrase/MutL, N-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1pvgA01
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	1pvgA02
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	1pvgB01
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	1pvgB02
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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8. Citations (1)

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Unit-cell length a length_a	58.456 Å
Unit-cell length b length_b	71.081 Å
Unit-cell length c length_c	216.132 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	8

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	29.750 Å
R factor r_factor	0.2087
R_work r_work	0.2057
R_free r_free	0.2415

fit	/app/data/saxs_computation/pv/1pvg/1pvg.fit
pddf	/app/data/pr_computation/pv/1pvg/1pvg.pr.out
profile	/app/data/saxs_computation/pv/1pvg/1pvg.dat

Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II

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

DNA topoisomerase II

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction