1yua

C-TERMINAL DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I

Method: SOLUTION NMR Dmax: 54.8 Å Quality: REASONABLE

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

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 745–865 Fragment:122 C-TERMINAL RESIDUES No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions Resolution not provided

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.

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 2–122; UniProt 745–865

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 1yua

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1yua
Deposition date deposition_date1995-03-02
Structure title titleC-TERMINAL DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I
Keywords keywordsGENE-REGULATING PROTEIN, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.34
Radius of gyration Rg (electron density) rg_electron15.05
Forward intensity I(0) i01778970000.00
Molecular weight molecular_weight359890.0 kDa
Excluded volume excluded_volume450680 ų
Envelope volume envelope_volume39036 ų
Hydration-shell volume shell_volume17943 ų
Envelope diameter envelope_diameter64.2
Shell Rg shell_rg24.60
Envelope Rg envelope_rg19.12
Shape Rg shape_rg14.99
Total Rg total_rg15.41
Total atoms total_atoms50518
Residues n_residues3172
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax54.8
Rg (real space) rg_real15.30
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real1.7790e+09
I(0) uncertainty (real space) i0_real_error2.0160e+07
Rg (reciprocal space) rg_reciprocal15.30
I(0) (reciprocal space) i0_reciprocal1779000000.0000
Solution quality estimate total_estimate0.6036
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.8
Skewness Skewness skewness0.233
Kurtosis Kurtosis kurtosis-0.268
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha380900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.721; Stabil: 0.995; Sysdev: 0.256; Positv: 1.000; Valcen: 0.924; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1yuaa1
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.3 — Zinc beta-ribbon
Family Family familyg.41.3.3 — Prokaryotic DNA topoisomerase I, a C-terminal fragment
Domain ID domain_idd1yuaa2
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.3 — Zinc beta-ribbon
Family Family familyg.41.3.3 — Prokaryotic DNA topoisomerase I, a C-terminal fragment

CATH v4.4 (2 domains)

Domain ID domain_id1yuaA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology65 — Bacterial Topoisomerase I; domain 1
Homologous superfamily homologous superfamily10 — Bacterial Topoisomerase I, domain 1
Domain ID domain_id1yuaA02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)