3we2

Structure of BLM RQC domain bound to a phosphate ion

Method: X-RAY DIFFRACTION Dmax: 75.6 Å Quality: GOOD

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

Bloom syndrome protein

Homo sapiens

UniProt P54132

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 1068–1209 Fragment:RecQ C-terminal (RQC) domain, UNP residues 1068-1209 PO4 PHOSPHATE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8.4;293 K;20-25% PEG 4000, 50mM sodium phosphate, 150mM sodium acetate, 100mM Tris-HCl, 15%(v/v) glycerol, pH 8.4, VAPOR DIFFUSION, temperature 293K Resolution 2.70 Å R-free 0.271
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1068–1209 Fragment:RecQ C-terminal (RQC) domain, UNP residues 1068-1209 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8.4;293 K;20-25% PEG 4000, 50mM sodium phosphate, 150mM sodium acetate, 100mM Tris-HCl, 15%(v/v) glycerol, pH 8.4, VAPOR DIFFUSION, temperature 293K Resolution 2.70 Å R-free 0.271

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.

12 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BLM_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–147; UniProt 1068–1209 Author chain B; PDBConstruct 6–147; UniProt 1068–1209

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 3we2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3we2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3we2
Deposition date deposition_date2013-06-28
Structure title titleStructure of BLM RQC domain bound to a phosphate ion
Keywords keywordsWinged-Helix, DNA helicase, DNA binding, DNA binding protein; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.05
Radius of gyration Rg (electron density) rg_electron21.32
Forward intensity I(0) i012612700.00
Molecular weight molecular_weight26305.0 kDa
Excluded volume excluded_volume32833 ų
Envelope volume envelope_volume40562 ų
Hydration-shell volume shell_volume16996 ų
Envelope diameter envelope_diameter79.1
Shell Rg shell_rg26.38
Envelope Rg envelope_rg21.45
Shape Rg shape_rg21.29
Total Rg total_rg22.12
Total atoms total_atoms1836
Residues n_residues232
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 dmax75.6
Rg (real space) rg_real22.15
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real1.2610e+07
I(0) uncertainty (real space) i0_real_error1.7450e+05
Rg (reciprocal space) rg_reciprocal22.13
I(0) (reciprocal space) i0_reciprocal12610000.0000
Solution quality estimate total_estimate0.7745
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.411
Kurtosis Kurtosis kurtosis-0.410
Angular range angular_range— – 0.3600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1836000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.745; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3we2A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id3we2B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

8. Citations (1)

9. Files and Curves (10)