SAXSdb — 3l4k

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

DNA topoisomerase 2

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–DNA Monomer Protein × 1 DNA 4 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 421–1177	Fragment：RESIDUES 421-1177 Non-standard monomer：Yes (specific site not provided by mmCIF)	;DNA (5'-D(PCPCPTPAPCPTPGPCPTPAPC)-3') ; × 1 ;DNA (5'-D(CPGPCPGPGPTPAPGPCPAPGPTPAPGPG)-3') ; × 1 ;DNA (5'-D(PGPGPAPTPGPAPCPGPAPTP)-3') ; × 1 ;DNA (5'-D(CPGPCPGPAPAPTPCPGPTPCPAPTPCPC)-3') ; × 1 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

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 3L4K	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 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 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 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
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 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
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 1–757； UniProt 421–1177

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3l4k
Deposition date deposition_date	2009-12-20
Structure title title	Topoisomerase II-DNA cleavage complex, metal-bound
Keywords keywords	;TOPOISOMERASE, PROTEIN-DNA COMPLEX, COVALENTLY LINKED COMPLEX, DNA SUPERCOILING, DNA REPLICATION, ATP-binding, DNA-binding, Isomerase, Nucleotide-binding, Nucleus, Phosphoprotein, Isomerase-DNA complex ;; Isomerase/DNA
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	31.57 Å
Radius of gyration Rg (electron density) rg_electron	31.68 Å
Forward intensity I(0) i0	143824000.00
Molecular weight molecular_weight	92486.0 kDa
Excluded volume excluded_volume	114350 Å³
Envelope volume envelope_volume	151840 Å³
Hydration-shell volume shell_volume	40751 Å³
Envelope diameter envelope_diameter	113.3 Å
Shell Rg shell_rg	37.89 Å
Envelope Rg envelope_rg	32.05 Å
Shape Rg shape_rg	31.68 Å
Total Rg total_rg	32.17 Å
Total atoms total_atoms	6466
Residues n_residues	746
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	107.0 Å
Rg (real space) rg_real	31.63 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	1.4380e+08
I(0) uncertainty (real space) i0_real_error	2.1870e+06
Rg (reciprocal space) rg_reciprocal	31.61 Å
I(0) (reciprocal space) i0_reciprocal	143800000.0000
Solution quality estimate total_estimate	0.8727
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.2 Å
Skewness Skewness skewness	0.428
Kurtosis Kurtosis kurtosis	-0.240
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27590000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.894

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	DNA topoisomerase 2
Molecular weight formula_weight	88025.2 kDa
EC 编号 ec_number	5.99.1.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7028

SRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	SACCHAROMYCES CEREVISIAE

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PCPCPTPAPCPTPGPCPTPAP*C)-3') ;
Molecular weight formula_weight	3269.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

CCTACTGCTAC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(CPGPCPGPGPTPAPGPCPAPGPTPAPGP*G)-3') ;
Molecular weight formula_weight	4675.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CGCGGTAGCAGTAGG

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(PGPGPAPTPGPAPCPGPAPTP*)-3') ;
Molecular weight formula_weight	3109.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GGATGACGAT

Entity 5 Entity 5 polymer

Description description	;DNA (5'-D(CPGPCPGPAPAPTPCPGPTPCPAPTPCP*C)-3') ;
Molecular weight formula_weight	4529.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CGCGAATCGTCATCC

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	3'-THIO-THYMIDINE-5'-PHOSPHATE
Molecular weight formula_weight	338.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3l4ka_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.11 — Type II DNA topoisomerase C-terminal domain-like
Superfamily Superfamily superfamily	e.11.1 — Type II DNA topoisomerase C-terminal domain-like
Family Family family	e.11.1.1 — Type II DNA topoisomerase C-terminal domain-like

CATH v4.4 (5 domains)

Domain ID domain_id	3l4kA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	670 —

Domain ID domain_id	3l4kA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3l4kA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	199 — Topoisomerase II; domain 5
Homologous superfamily homologous superfamily	10 — Topoisomerase II, domain 5

Domain ID domain_id	3l4kA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3l4kA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	268 — Topoisomerase; domain 3
Homologous superfamily homologous superfamily	10 — Topoisomerase, domain 3

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8. Citations (1)

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Unit-cell length a length_a	86.064 Å
Unit-cell length b length_b	91.851 Å
Unit-cell length c length_c	115.939 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	4

Space group space_group	P 21 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.980 Å
Low-resolution limit resolution_low	49.023 Å
R factor r_factor	0.2408
R_work r_work	0.2391
R_free r_free	0.2733

fit	/app/data/saxs_computation/l4/3l4k/3l4k.fit
pddf	/app/data/pr_computation/l4/3l4k/3l4k.pr.out
profile	/app/data/saxs_computation/l4/3l4k/3l4k.dat

Topoisomerase II-DNA cleavage complex, metal-bound

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

DNA topoisomerase 2

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

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (1 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)