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1cyy

CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM

Method: X-RAY DIFFRACTION Dmax: 79.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA TOPOISOMERASE I

Escherichia coli

UniProt P06612

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 214–477 Chain B； UniProt 214–477 Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III 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
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 214–477 Chain B； UniProt 214–477 Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III 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
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 214–477 Chain B； UniProt 214–477 Fragment：30 KDA FRAGMENT COMPRISING DOMAINS II AND III 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

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 1CYY 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 construct Different mutation/modification 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 1–597（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 construct Different mutation/modification 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 1–597（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 construct Different mutation/modification 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 1–597（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 construct Different mutation/modification 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 1–597（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 construct Different mutation/modification 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 1–597（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 construct Different mutation/modification 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 1–597（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
1CY8 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE AND 3'-THYMIDINE MONOPHOSPHATE 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 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 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
1CY9 CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM Deposited 1999-08-31 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
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–597（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 oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–596（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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 19 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 1–264； UniProt 214–477 Author chain B； PDBConstruct 1–264； UniProt 214–477

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1cyy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1cyy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1cyy
Deposition date deposition_date1999-08-31
Structure title titleCRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM
Keywords keywordsDNA TOPOISOMERASE, DECATENATING ENZYME, ISOMERASE; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.83 Å
Radius of gyration Rg (electron density) rg_electron25.67 Å
Forward intensity I(0) i053409600.00
Molecular weight molecular_weight56106.0 kDa
Excluded volume excluded_volume70056 ų
Envelope volume envelope_volume89060 ų
Hydration-shell volume shell_volume29126 ų
Envelope diameter envelope_diameter83.5 Å
Shell Rg shell_rg32.74 Å
Envelope Rg envelope_rg25.23 Å
Shape Rg shape_rg25.64 Å
Total Rg total_rg26.56 Å
Total atoms total_atoms3940
Residues n_residues501
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax79.0 Å
Rg (real space) rg_real26.67 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real5.3410e+07
I(0) uncertainty (real space) i0_real_error6.4160e+05
Rg (reciprocal space) rg_reciprocal26.72 Å
I(0) (reciprocal space) i0_reciprocal53410000.0000
Solution quality estimate total_estimate0.9165
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary77.7 Å
Skewness Skewness skewness0.077
Kurtosis Kurtosis kurtosis-0.650
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7966000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.987; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.951
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1cyya_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.10 — Prokaryotic type I DNA topoisomerase
Superfamily Superfamily superfamilye.10.1 — Prokaryotic type I DNA topoisomerase
Family Family familye.10.1.1 — Prokaryotic type I DNA topoisomerase
Domain ID domain_idd1cyyb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.10 — Prokaryotic type I DNA topoisomerase
Superfamily Superfamily superfamilye.10.1 — Prokaryotic type I DNA topoisomerase
Family Family familye.10.1.1 — Prokaryotic type I DNA topoisomerase

CATH v4.4 (4 domains)

Domain ID domain_id1cyyA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology290 — Topoisomerase I; domain 4
Homologous superfamily homologous superfamily10 — Topoisomerase I, domain 4
Domain ID domain_id1cyyA02
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase I, domain 3
Domain ID domain_id1cyyB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology290 — Topoisomerase I; domain 4
Homologous superfamily homologous superfamily10 — Topoisomerase I, domain 4
Domain ID domain_id1cyyB02
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase I, domain 3
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8. Citations (1)

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9. Files and Curves (10)