1vcc

AMINO TERMINAL 9KDA DOMAIN OF VACCINIA VIRUS DNA TOPOISOMERASE I RESIDUES 1-77, EXPERIMENTAL ELECTRON DENSITY FOR RESIDUES 1-77

Method: X-RAY DIFFRACTION D_max: 44.0 Å Quality: GOOD

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

DNA TOPOISOMERASE I

Vaccinia virus

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 1–77	Fragment：AMINO TERMINAL 9KDA, RESIDUES 1 - 77	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.60 Å R-free 0.287

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 1VCC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A41 TYPE 1-TOPOISOMERASE CATALYTIC FRAGMENT FROM VACCINIA VIRUS Deposited 1998-02-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 81–314（234 aa） Fragment：CARBOXY-TERMINAL CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.30 Å R-free 0.309

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOP1_VACCV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–77； UniProt 1–77

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1vcc
Deposition date deposition_date	1995-10-02
Structure title title	AMINO TERMINAL 9KDA DOMAIN OF VACCINIA VIRUS DNA TOPOISOMERASE I RESIDUES 1-77, EXPERIMENTAL ELECTRON DENSITY FOR RESIDUES 1-77
Keywords keywords	DNA BINDING; DNA BINDING
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	13.78 Å
Radius of gyration Rg (electron density) rg_electron	12.26 Å
Forward intensity I(0) i0	1741970.00
Molecular weight molecular_weight	9036.0 kDa
Excluded volume excluded_volume	11381 Å³
Envelope volume envelope_volume	12647 Å³
Hydration-shell volume shell_volume	9133 Å³
Envelope diameter envelope_diameter	42.0 Å
Shell Rg shell_rg	17.43 Å
Envelope Rg envelope_rg	12.59 Å
Shape Rg shape_rg	12.20 Å
Total Rg total_rg	13.74 Å
Total atoms total_atoms	640
Residues n_residues	77
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	44.0 Å
Rg (real space) rg_real	13.70 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.7420e+06
I(0) uncertainty (real space) i0_real_error	1.9600e+04
Rg (reciprocal space) rg_reciprocal	13.70 Å
I(0) (reciprocal space) i0_reciprocal	1742000.0000
Solution quality estimate total_estimate	0.8949
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.113
Kurtosis Kurtosis kurtosis	-0.417
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	259800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.953

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1vcca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.121 — DNA topoisomerase I domain
Superfamily Superfamily superfamily	d.121.1 — DNA topoisomerase I domain
Family Family family	d.121.1.1 — Vaccinia DNA topoisomerase I, 9 kDa N-terminal fragment

CATH v4.4 (1 domains)

Domain ID domain_id	1vccA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	66 — Viral Topoisomerase I
Homologous superfamily homologous superfamily	10 — DNA topoisomerase I domain

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8. Citations (1)

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Unit-cell length a length_a	32.460 Å
Unit-cell length b length_b	42.510 Å
Unit-cell length c length_c	60.850 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	1.600 Å
Low-resolution limit resolution_low	5.000 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2870

Description description	DNA TOPOISOMERASE I
Molecular weight formula_weight	9066.3 kDa
EC 编号 ec_number	5.99.1.2
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	702

AMINO TERMINAL 9KDA DOMAIN OF VACCINIA VIRUS DNA TOPOISOMERASE I RESIDUES 1-77, EXPERIMENTAL ELECTRON DENSITY FOR RESIDUES 1-77

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Vaccinia virus
NCBI Class编号 ncbi_taxonomy_id	10254
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	62

fit	/app/data/saxs_computation/vc/1vcc/1vcc.fit
pddf	/app/data/pr_computation/vc/1vcc/1vcc.pr.out
profile	/app/data/saxs_computation/vc/1vcc/1vcc.dat