SAXSdb — 1cy8

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

DNA TOPOISOMERASE I

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–597	Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I	PO4 PHOSPHATE ION × 1 T3P THYMIDINE-3'-PHOSPHATE × 1 TMP THYMIDINE-5'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；2.2M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 2.45 Å R-free 0.295

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 1CY8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CY0 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3'-5'-ADENOSINE DIPHOSPHATE Deposited 1999-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I	Not recorded	A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 5；287 K；2.14M ammonium sulfate, pH 5.0, MICRODIALYSIS, temperature 287K	Resolution 2.45 Å R-free 0.274
1CY1 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'PTPTPT Deposited 1999-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I	Not recorded	PO4 PHOSPHATE ION × 1 TMP THYMIDINE-5'-PHOSPHATE × 2 THP THYMIDINE-3',5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；2.3M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 2.30 Å R-free 0.307
1CY2 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH TPTPTP3' Deposited 1999-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I	Not recorded	PO4 PHOSPHATE ION × 1 TMP THYMIDINE-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；2.3M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 2.30 Å R-free 0.284
1CY4 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpTp3' Deposited 1999-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I	Not recorded	PO4 PHOSPHATE ION × 3 TMP THYMIDINE-5'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；2.2M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.55 Å R-free 0.299
1CY6 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3' THYMIDINE MONOPHOSPHATE Deposited 1999-08-31	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I	Not recorded	PO4 PHOSPHATE ION × 3 T3P THYMIDINE-3'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；2.2M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 2.50 Å R-free 0.309
1CY7 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE Deposited 1999-08-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–597（597 aa） Fragment：67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I	Mutation：GLY-SER ATTACHED AT N-TERMINUS DUE TO CONSTRUCT	PO4 PHOSPHATE ION × 1 TMP THYMIDINE-5'-PHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；2.3M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.295
1CY9 CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM Deposited 1999-08-31	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 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III Chain B 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；11-13%(W/V) PEG 3500, 20MM MES PH 6.0, 50MM KCL, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.242
1CYY CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM Deposited 1999-08-31	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 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III Chain B 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；2M AMMONIUM SULFATE, 100MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.15 Å R-free 0.282
1CYY CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM Deposited 1999-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III Chain B 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；2M AMMONIUM SULFATE, 100MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.15 Å R-free 0.282
1CYY CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM Deposited 1999-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III Chain B 214–477（264 aa） Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；296 K；2M AMMONIUM SULFATE, 100MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.15 Å R-free 0.282
1ECL AMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE I (RESIDUES 2-590 OF MATURE PROTEIN) CLONING ARTIFACT ADDS TWO RESIDUES TO THE AMINO-TERMINUS WHICH WERE NOT OBSERVED IN THE EXPERIMENTAL ELECTRON DENSITY (GLY-2, SER-1). Deposited 1995-05-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–597（597 aa）	Mutation：GLY SER INSERTION AT N-TERMINUS, INSERTION OF STOP CODON AT 598; ENGINEERED	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1MW8 Crystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I and 5'-ACTTCGGGATG-3' Deposited 2002-09-27	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: dimeric	Chain X 1–592（592 aa） Fragment：67 kDa N-terminal fragment	Mutation：H365R	SO4 SULFATE ION × 5 TMP THYMIDINE-5'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；287 K；ammonium sulfate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 1.90 Å R-free 0.273
1MW9 Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I Deposited 2002-09-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–592（592 aa） Fragment：67 kDa N-terminal fragment	Mutation：H365R	SO4 SULFATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions DIALYSIS；pH 8；287 K；ammonium sulfate, pH 8, DIALYSIS, temperature 287K	Resolution 1.67 Å R-free 0.216
1YUA C-TERMINAL DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I Deposited 1995-03-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 745–865（121 aa） Fragment：122 C-TERMINAL RESIDUES	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
3PWT Crystal structure of mutant E.coli topoisomerase IA Deposited 2010-12-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–596（596 aa） Fragment：N-terminal catalytical domain, 67K	Mutation：D111N	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；288 K；2M ammonium sulfate, pH 7.4, VAPOR DIFFUSION, temperature 288K	Resolution 1.90 Å R-free 0.249
9GDA RNAP-TopoI complex on duplex scaffold Deposited 2024-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain F 1–865（865 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9GDB RNAP-TopoI complex on bubble scaffold - consensus reconstruction Deposited 2024-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain F 1–865（865 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9GDC RNAP-TopoI complex on bubble scaffold - single-bubble configuration Deposited 2024-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain F 1–865（865 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
9GDD RNAP-TopoI complex on bubble scaffold - two-bubble configuration Deposited 2024-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain F 1–865（865 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
9GDE RNAP-TopoI complex on long-overhang scaffold - orientation 1 Deposited 2024-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain F 1–865（865 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9GDH RNAP-TopoI complex on long-overhang scaffold - orientation 2 Deposited 2024-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric	Chain F 1–865（865 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

19 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOP1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–599； UniProt 1–597

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	1cy8
Deposition date deposition_date	1999-08-31
Structure title title	COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE AND 3'-THYMIDINE MONOPHOSPHATE
Keywords keywords	DNA TOPOISOMERASE, RELAXING ENZYME, 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	30.38 Å
Radius of gyration Rg (electron density) rg_electron	30.05 Å
Forward intensity I(0) i0	70592200.00
Molecular weight molecular_weight	64528.0 kDa
Excluded volume excluded_volume	80285 Å³
Envelope volume envelope_volume	107900 Å³
Hydration-shell volume shell_volume	31383 Å³
Envelope diameter envelope_diameter	105.9 Å
Shell Rg shell_rg	35.38 Å
Envelope Rg envelope_rg	29.99 Å
Shape Rg shape_rg	30.07 Å
Total Rg total_rg	30.52 Å
Total atoms total_atoms	4538
Residues n_residues	563
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	101.8 Å
Rg (real space) rg_real	30.48 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	7.0590e+07
I(0) uncertainty (real space) i0_real_error	1.1230e+06
Rg (reciprocal space) rg_reciprocal	30.44 Å
I(0) (reciprocal space) i0_reciprocal	70590000.0000
Solution quality estimate total_estimate	0.8826
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.3 Å
Skewness Skewness skewness	0.394
Kurtosis Kurtosis kurtosis	-0.386
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10210000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.894

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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	DNA TOPOISOMERASE I
Molecular weight formula_weight	67542.5 kDa
EC 编号 ec_number	5.99.1.2
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	4799

GSMGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSI

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	THYMIDINE-3'-PHOSPHATE
Molecular weight formula_weight	322.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	THYMIDINE-5'-PHOSPHATE
Molecular weight formula_weight	322.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	261

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cy8a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.10 — Prokaryotic type I DNA topoisomerase
Superfamily Superfamily superfamily	e.10.1 — Prokaryotic type I DNA topoisomerase
Family Family family	e.10.1.1 — Prokaryotic type I DNA topoisomerase

CATH v4.4 (4 domains)

Domain ID domain_id	1cy8A01
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	1cy8A02
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	1cy8A03
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	1cy8A04
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	63.610 Å
Unit-cell length b length_b	79.270 Å
Unit-cell length c length_c	141.510 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 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	19.820 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2950

fit	/app/data/saxs_computation/cy/1cy8/1cy8.fit
pddf	/app/data/pr_computation/cy/1cy8/1cy8.pr.out
profile	/app/data/saxs_computation/cy/1cy8/1cy8.dat

COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE AND 3'-THYMIDINE MONOPHOSPHATE

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

DNA TOPOISOMERASE I

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