SAXSdb — 1es8

▼

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

RESTRICTION ENDONUCLEASE BGLII

Bacillus subtilis

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–223	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；30% isopropanol, 0.2 M sodium acetate, 0.1 M Bis-tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.258

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 1ES8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D2I CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BGLII COMPLEXED WITH DNA 16-MER Deposited 1999-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–223（223 aa） Chain B 1–223（223 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5.2；293 K；15- 20% PEG 4000, 0.2 M AMMONIUM SULFATE, 0.1 M MES PH 5.2, MICROBATCH, temperature 293K	Resolution 1.70 Å R-free 0.200
1DFM Crystal structure of restriction endonuclease BGLII complexed with DNA 16-mer Deposited 1999-12-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–223（223 aa） Fragment：BGLII Chain B 1–223（223 aa） Fragment：BGLII	Mutation：SELENOMETHIONYL (MSE FOR MET) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：SELENOMETHIONYL (MSE FOR MET) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；15- 20% PEG 4000, 0.2 M (NH4)2SO4, 0.1 M MES PH 5.2. CRYSTALS WERE LATER SOAKED WITH 5MM CACL2., VAPOR DIFFUSION, HANGING DROP	Resolution 1.50 Å R-free 0.224

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	T2B2_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–223； UniProt 1–223

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1es8
Deposition date deposition_date	2000-04-07
Structure title title	Crystal structure of free BglII
Keywords keywords	RESTRICTION ENDONUCLEASE, RESTRICTION ENZYME, uncomplexed, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.72 Å
Radius of gyration Rg (electron density) rg_electron	16.58 Å
Forward intensity I(0) i0	9173330.00
Molecular weight molecular_weight	22783.0 kDa
Excluded volume excluded_volume	28665 Å³
Envelope volume envelope_volume	32794 Å³
Hydration-shell volume shell_volume	16519 Å³
Envelope diameter envelope_diameter	54.5 Å
Shell Rg shell_rg	22.61 Å
Envelope Rg envelope_rg	16.90 Å
Shape Rg shape_rg	16.60 Å
Total Rg total_rg	17.55 Å
Total atoms total_atoms	1596
Residues n_residues	193
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

▼

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

Maximum dimension Dmax dmax	55.9 Å
Rg (real space) rg_real	17.61 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	9.1730e+06
I(0) uncertainty (real space) i0_real_error	1.0890e+05
Rg (reciprocal space) rg_reciprocal	17.62 Å
I(0) (reciprocal space) i0_reciprocal	9173000.0000
Solution quality estimate total_estimate	0.8871
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.173
Kurtosis Kurtosis kurtosis	-0.377
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2262000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.926

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	RESTRICTION ENDONUCLEASE BGLII
Molecular weight formula_weight	26031.8 kDa
EC 编号 ec_number	3.1.21.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1677

MKIDITDYNHADEILNPQLWKEIEETLLKMPLHVKASDQASKVGSLIFDPVGTNQYIKDELVPKHWKNNIPIPKRFDFLGTDIDFGKRDTLVEVQFSNYPFLLNNTVRSELFHKSNMDIDEEGMKVAIIITKGHMFPASNSSLYYEQAQNQLNSLAEYNVFDVPIRLVGLIEDFETDIDIVSTTYADKRYSRTITKRDTVKGKVIDTNTPNTRRRKRGTIVTY

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1es8a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.5 — Restriction endonuclease BglII

CATH v4.4 (1 domains)

Domain ID domain_id	1es8A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	20 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	79.150 Å
Unit-cell length b length_b	79.150 Å
Unit-cell length c length_c	66.520 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2140
R_free r_free	0.2580

fit	/app/data/saxs_computation/es/1es8/1es8.fit
pddf	/app/data/pr_computation/es/1es8/1es8.pr.out
profile	/app/data/saxs_computation/es/1es8/1es8.dat

Crystal structure of free BglII

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

RESTRICTION ENDONUCLEASE BGLII

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

Diffraction experiment Diffraction