3ueo

Crystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide

Method: X-RAY DIFFRACTION Dmax: 101.5 Å Quality: REASONABLE

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

DNA topoisomerase 2-binding protein 1

Homo sapiens

UniProt Q92547

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 549–746 Chain C; UniProt 549–746 Fragment:BRCT domain phospho-peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;PEG 10000, Ammonium acetate, bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.60 Å R-free 0.234
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 549–746 Chain D; UniProt 549–746 Fragment:BRCT domain phospho-peptide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;PEG 10000, Ammonium acetate, bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.60 Å R-free 0.234

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.

14 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOPB1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–203; UniProt 549–746 Author chain B; PDBConstruct 6–203; UniProt 549–746 Author chain C; PDBConstruct 6–203; UniProt 549–746 Author chain D; PDBConstruct 6–203; UniProt 549–746

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 3ueo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ueo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ueo
Deposition date deposition_date2011-10-31
Structure title titleCrystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide
Keywords keywordsBRCT domain, phospho-peptide binding, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.24
Radius of gyration Rg (electron density) rg_electron30.64
Forward intensity I(0) i0108714000.00
Molecular weight molecular_weight83663.0 kDa
Excluded volume excluded_volume105340 ų
Envelope volume envelope_volume138340 ų
Hydration-shell volume shell_volume38524 ų
Envelope diameter envelope_diameter106.3
Shell Rg shell_rg36.81
Envelope Rg envelope_rg30.65
Shape Rg shape_rg30.60
Total Rg total_rg31.35
Total atoms total_atoms5875
Residues n_residues758
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 dmax101.5
Rg (real space) rg_real31.21
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real1.0870e+08
I(0) uncertainty (real space) i0_real_error1.7220e+06
Rg (reciprocal space) rg_reciprocal31.22
I(0) (reciprocal space) i0_reciprocal108700000.0000
Solution quality estimate total_estimate0.6898
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.8
Skewness Skewness skewness0.319
Kurtosis Kurtosis kurtosis-0.332
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18480000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.994; Smooth: 0.938

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id3ueoA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ueoA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ueoB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ueoB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ueoC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ueoC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ueoD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ueoD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain

8. Citations (1)

9. Files and Curves (10)