SAXSdb — 2o5c

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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 1–653	Not recorded	5'-D(CPGPCPAPAPCPTPT)-3' × 1 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
2	Protein–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 1–653	Not recorded	5'-D(CPGPCPAPAPCPTPT)-3' × 1 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

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 2O5C	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 construct 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 construct 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
11KB E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo AACTGTTG Deposited 2026-02-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–640（640 aa）	Not recorded	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
11LB E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo GCAACTGG Deposited 2026-03-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–640（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 construct 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 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 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 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 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 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 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 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
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 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 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 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOP3_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–653； UniProt 1–653 Author chain B； PDBConstruct 1–653； UniProt 1–653

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	2o5c
Deposition date deposition_date	2006-12-05
Structure title title	Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 5.5
Keywords keywords	topoisomerase type IA complex with ssDNA, 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	40.57 Å
Radius of gyration Rg (electron density) rg_electron	40.59 Å
Forward intensity I(0) i0	342340000.00
Molecular weight molecular_weight	147120.0 kDa
Excluded volume excluded_volume	182780 Å³
Envelope volume envelope_volume	260180 Å³
Hydration-shell volume shell_volume	54878 Å³
Envelope diameter envelope_diameter	135.3 Å
Shell Rg shell_rg	44.60 Å
Envelope Rg envelope_rg	40.04 Å
Shape Rg shape_rg	40.59 Å
Total Rg total_rg	40.80 Å
Total atoms total_atoms	10349
Residues n_residues	1279
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	131.8 Å
Rg (real space) rg_real	40.61 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	3.4230e+08
I(0) uncertainty (real space) i0_real_error	6.5100e+06
Rg (reciprocal space) rg_reciprocal	40.57 Å
I(0) (reciprocal space) i0_reciprocal	342300000.0000
Solution quality estimate total_estimate	0.8907
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.3 Å
Skewness Skewness skewness	0.309
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41860000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.815

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	5'-D(CPGPCPAPAPCPTPT)-3'
Molecular weight formula_weight	2386.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	10705

CGCAACTT

Entity 2 Entity 2 polymer

Description description	DNA topoisomerase 3
Molecular weight formula_weight	74151.7 kDa
EC 编号 ec_number	5.99.1.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKKSPPADEVGSGAIAHHHHHH

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 3 Entity 3 non-polymer

Description description	THYMINE
Molecular weight formula_weight	126.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	356

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2o5cA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2o5cA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	460 — Topoisomerase I; domain 2
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 2

Domain ID domain_id	2o5cA03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 3

Domain ID domain_id	2o5cA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	290 — Topoisomerase I; domain 4
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 4

Domain ID domain_id	2o5cB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2o5cB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	460 — Topoisomerase I; domain 2
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 2

Domain ID domain_id	2o5cB03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 3

Domain ID domain_id	2o5cB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	290 — Topoisomerase I; domain 4
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 4

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8. Citations (1)

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Unit-cell length a length_a	102.210 Å
Unit-cell length b length_b	102.210 Å
Unit-cell length c length_c	443.750 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	29.147 Å
R factor r_factor	0.2090
R_work r_work	0.2070
R_free r_free	0.2450

fit	/app/data/saxs_computation/o5/2o5c/2o5c.fit
pddf	/app/data/pr_computation/o5/2o5c/2o5c.pr.out
profile	/app/data/saxs_computation/o5/2o5c/2o5c.dat

Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 5.5

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)