1dc1

RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD

Method: X-RAY DIFFRACTION Dmax: 84.7 Å Quality: EXCELLENT

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

BSOBI RESTRICTION ENDONUCLEASE

Geobacillus stearothermophilus

UniProt P70985

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 1–323 Chain B; UniProt 1–323 Not recorded ;DNA (5'-D(*T*AP*TP*AP*CP*TP*CP*GP*AP*GP*TP*AP*T)-3') ; × 2 DIO 1,4-DIETHYLENE DIOXIDE × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.6;293 K;EQUILIBRATION AGAINST RESERVOIR OF 20% (V/V) DIOXANE, 2% (V/V) ETHYLENE GLYCOL AND 5 MM DTT. DROPS WERE FORMED BY MIXING 2.5 UL PROTEIN-DNA COMPLEX (10 MG/ML PROTEIN; 1.1 FOLD MOLAR EXCESS DNA) IN BUFFER (20 MM TRIS-HCL PH 7.6, 300 MM NACL, 0.1 MM EDTA, 1 MM DTT, 0.02% NA AZIDE) WITH 2.5 UL DISTILLED WATER, 2.5 UL RESERVOIR SOLUTION AND 1.5 UL 350 MM N-HEPTYL-B-D-GLUCOSIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K Resolution 1.70 Å R-free 0.253

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name T2B1_BACST
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–323; UniProt 1–323 Author chain B; PDBConstruct 1–323; UniProt 1–323

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 1dc1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dc1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dc1
Deposition date deposition_date1999-11-04
Structure title titleRESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD
Keywords keywordsPROTEIN-DNA COMPLEX, RESTRICTION ENDONUCLEASE, THERMOPHILIC ENZYME, DEGENERATE DNA RECOGNITION, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.65
Radius of gyration Rg (electron density) rg_electron26.31
Forward intensity I(0) i0107284000.00
Molecular weight molecular_weight78640.0 kDa
Excluded volume excluded_volume97217 ų
Envelope volume envelope_volume114480 ų
Hydration-shell volume shell_volume35363 ų
Envelope diameter envelope_diameter89.4
Shell Rg shell_rg34.47
Envelope Rg envelope_rg26.63
Shape Rg shape_rg26.34
Total Rg total_rg27.03
Total atoms total_atoms5513
Residues n_residues646
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 dmax84.7
Rg (real space) rg_real26.55
Rg uncertainty (real space) rg_real_error0.38
I(0) (real space) i0_real1.0730e+08
I(0) uncertainty (real space) i0_real_error1.4010e+06
Rg (reciprocal space) rg_reciprocal26.58
I(0) (reciprocal space) i0_reciprocal107300000.0000
Solution quality estimate total_estimate0.9008
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.246
Kurtosis Kurtosis kurtosis-0.445
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24850000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1dc1a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.11 — Restriction endonuclease BsobI
Domain ID domain_idd1dc1b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.11 — Restriction endonuclease BsobI

CATH v4.4 (4 domains)

Domain ID domain_id1dc1A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology91 — Restriction Endonuclease
Homologous superfamily homologous superfamily10
Domain ID domain_id1dc1A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily90 — Restriction endonuclease BsobI, helical domain
Domain ID domain_id1dc1B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology91 — Restriction Endonuclease
Homologous superfamily homologous superfamily10
Domain ID domain_id1dc1B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily90 — Restriction endonuclease BsobI, helical domain

8. Citations (2)

9. Files and Curves (10)