SAXSdb — 1dfm

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

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–223 Chain B； UniProt 1–223	Fragment：BGLII Mutation：SELENOMETHIONYL (MSE FOR MET) Non-standard monomer：Yes (specific site not provided by mmCIF)	;DNA (5'-D(TPAPTPTPAPTPAPGPAPTPCPTPAPTPAPA)-3') ; × 2 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

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 1DFM	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 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
1ES8 Crystal structure of free BglII Deposited 2000-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–223（223 aa）	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

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	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–223； UniProt 1–223 Author chain B； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dfm
Deposition date deposition_date	1999-12-06
Structure title title	Crystal structure of restriction endonuclease BGLII complexed with DNA 16-mer
Keywords keywords	RESTRICTION ENDONUCLEASE, RESTRICTION ENZYME, PROTEIN-DNA COMPLEX, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.21 Å
Radius of gyration Rg (electron density) rg_electron	22.58 Å
Forward intensity I(0) i0	72870500.00
Molecular weight molecular_weight	61236.0 kDa
Excluded volume excluded_volume	73927 Å³
Envelope volume envelope_volume	86397 Å³
Hydration-shell volume shell_volume	30563 Å³
Envelope diameter envelope_diameter	74.2 Å
Shell Rg shell_rg	30.88 Å
Envelope Rg envelope_rg	22.87 Å
Shape Rg shape_rg	22.58 Å
Total Rg total_rg	23.39 Å
Total atoms total_atoms	4242
Residues n_residues	463
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

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

Maximum dimension Dmax dmax	73.1 Å
Rg (real space) rg_real	23.06 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	7.2870e+07
I(0) uncertainty (real space) i0_real_error	8.9150e+05
Rg (reciprocal space) rg_reciprocal	23.10 Å
I(0) (reciprocal space) i0_reciprocal	72870000.0000
Solution quality estimate total_estimate	0.8931
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.2 Å
Skewness Skewness skewness	0.169
Kurtosis Kurtosis kurtosis	-0.402
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18780000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPAPTPTPAPTPAPGPAPTPCPTPAPTPAPA)-3') ;
Molecular weight formula_weight	4895.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	4850

TATTATAGATCTATAA

Entity 2 Entity 2 polymer

Description description	ENDONUCLEASE BGLII
Molecular weight formula_weight	26031.8 kDa
Mutation mutation	SELENOMETHIONYL (MSE FOR MET)
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

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 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	608

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dfma_
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

Domain ID domain_id	d1dfmb_
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 (2 domains)

Domain ID domain_id	1dfmA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1dfmB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	48.700 Å
Unit-cell length b length_b	101.800 Å
Unit-cell length c length_c	116.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2240

fit	/app/data/saxs_computation/df/1dfm/1dfm.fit
pddf	/app/data/pr_computation/df/1dfm/1dfm.pr.out
profile	/app/data/saxs_computation/df/1dfm/1dfm.dat

Crystal structure of restriction endonuclease BGLII complexed with DNA 16-mer

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

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)