SAXSdb — 11kb

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

DNA topoisomerase 3

Escherichia coli

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 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1–640	Not recorded	;DNA (5'-D(CPGPCPAPAPCPTPT)-3') ; × 1 ACT ACETATE ION × 1 FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.1M Lithium Acetate, 20%(w/v) PEG3350	Resolution 1.90 Å R-free 0.228

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 11KB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11FC E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo CTGAACTT Deposited 2026-02-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–640（640 aa）	Not recorded	MLI MALONATE ION × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286 K；0.2M Ammonium Citrate Dibasic, 20% (w/v) PEG 3350	Resolution 2.10 Å R-free 0.265
11GX E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo CGCAACTT Deposited 2026-02-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–640（640 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M Sodium Citrate, 20%(w/v) PEG4000, 20% (v/v) 2-Propanol	Resolution 2.22 Å R-free 0.261
11LB E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo GCAACTGG Deposited 2026-03-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–640（640 aa）	Not recorded	GOL GLYCEROL × 8 EDO 1,2-ETHANEDIOL × 2 FLC CITRATE ANION × 1 ACT ACETATE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M Sodium Citrate, 20%(w/V)PEG 4000, 10% (v/v) 2-Propanol	Resolution 1.85 Å R-free 0.212
11YY E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo ACTGACTT Deposited 2026-03-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–640（640 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 SIN SUCCINIC ACID × 1 CL CHLORIDE ION × 1 MLA MALONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；289 K；0.2M Ammonium Citrate Dibasic, 20% (w/v) PEG3350	Resolution 2.20 Å R-free 0.236
1D6M CRYSTAL STRUCTURE OF E. COLI DNA TOPOISOMERASE III Deposited 1999-10-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–653（653 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 6.3；287 K；1.65M Na, potassium phosphate, pH 6.3, MICRODIALYSIS, temperature 287K	Resolution 3.00 Å R-free 0.268
1I7D NONCOVALENT COMPLEX OF E.COLI DNA TOPOISOMERASE III WITH AN 8-BASE SINGLE-STRANDED DNA OLIGONUCLEOTIDE Deposited 2001-03-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–653（653 aa）	Mutation：Y328F	CL CHLORIDE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；1.3M ammonium sulfate, 0.8M sodium chloride, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.05 Å R-free 0.260
2O19 Structure of E. coli topoisomersae III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 5.5 Deposited 2006-11-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–653（653 aa） Fragment：E. coli topoisomerse III	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；1.5 M (NH4)SO4, 0.1 M Sodium citrate, 0.5 m NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.45 Å R-free 0.246
2O19 Structure of E. coli topoisomersae III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 5.5 Deposited 2006-11-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–653（653 aa） Fragment：E. coli topoisomerse III	Not recorded	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；1.5 M (NH4)SO4, 0.1 M Sodium citrate, 0.5 m NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.45 Å R-free 0.246
2O54 Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 7.0 Deposited 2006-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–653（653 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.5 M (NH4)SO4, 0.1 M Sodium citrate, 0.5 M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.269
2O54 Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol at pH 7.0 Deposited 2006-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–653（653 aa）	Not recorded	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.5 M (NH4)SO4, 0.1 M Sodium citrate, 0.5 M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.269
2O59 Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol pH 8.0 Deposited 2006-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–653（653 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；1.5 M (NH4)SO4, 0.1 M Sodium citrate, 0.5 M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.258
2O59 Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol pH 8.0 Deposited 2006-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–653（653 aa）	Not recorded	CL CHLORIDE ION × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；1.5 M (NH4)SO4, 0.1 M Sodium citrate, 0.5 M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.258
2O5C Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 5.5 Deposited 2006-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–653（653 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；1.5 M (NH4)SO4, 0.1M Sodium citrate, 0.5 M NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.35 Å R-free 0.245
2O5C Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 5.5 Deposited 2006-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–653（653 aa）	Not recorded	TDR THYMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；1.5 M (NH4)SO4, 0.1M Sodium citrate, 0.5 M NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.35 Å R-free 0.245
2O5E Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 7.0 Deposited 2006-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–653（653 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.5 M (NH4)SO4, 0.1M Sodium citrate, 0.5 NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.260
2O5E Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 7.0 Deposited 2006-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–653（653 aa）	Not recorded	TDR THYMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.5 M (NH4)SO4, 0.1M Sodium citrate, 0.5 NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.260

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOP3_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–640； UniProt 1–640

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	11kb
Deposition date deposition_date	2026-02-27
最后修订 last_revision	2026-04-29
Structure title title	E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo AACTGTTG
Keywords keywords	EcTopo3, ssDNA complex, ISOMERASE, 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	30.25 Å
Radius of gyration Rg (electron density) rg_electron	29.81 Å
Forward intensity I(0) i0	86503300.00
Molecular weight molecular_weight	71947.0 kDa
Excluded volume excluded_volume	89635 Å³
Envelope volume envelope_volume	117540 Å³
Hydration-shell volume shell_volume	34085 Å³
Envelope diameter envelope_diameter	103.3 Å
Shell Rg shell_rg	35.69 Å
Envelope Rg envelope_rg	29.62 Å
Shape Rg shape_rg	29.82 Å
Total Rg total_rg	30.33 Å
Total atoms total_atoms	5060
Residues n_residues	625
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	102.5 Å
Rg (real space) rg_real	30.31 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	8.6500e+07
I(0) uncertainty (real space) i0_real_error	1.4150e+06
Rg (reciprocal space) rg_reciprocal	30.28 Å
I(0) (reciprocal space) i0_reciprocal	86500000.0000
Solution quality estimate total_estimate	0.8788
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.287
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15910000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.907

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	DNA topoisomerase 3
Molecular weight formula_weight	72965.4 kDa
EC 编号 ec_number	5.6.2.1
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	5542

MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKKENLYFQ

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPGPCPAPAPCPTPT)-3') ;
Molecular weight formula_weight	2441.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

AACTGTTG

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	401

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8. Citations (2)

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Unit-cell length a length_a	38.966 Å
Unit-cell length b length_b	123.124 Å
Unit-cell length c length_c	86.255 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	42.640 Å
R factor r_factor	0.1907
R_work r_work	0.1888
R_free r_free	0.2281

fit	/app/data/saxs_computation/1k/11kb/11kb.fit
pddf	/app/data/pr_computation/1k/11kb/11kb.pr.out
profile	/app/data/saxs_computation/1k/11kb/11kb.dat

E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo AACTGTTG

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

DNA topoisomerase 3

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)