SAXSdb — 1dmu

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

BGLI RESTRICTION ENDONUCLEASE

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(APTPCPGPCPCPTPAPAPTPAPGPGPCPGPAP*T)-3') ; × 2 CALCIUM ION × 8 BETA-MERCAPTOETHANOL × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	T2B1_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–299； UniProt 1–299

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	1dmu
Deposition date deposition_date	1999-12-15
Structure title title	Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence
Keywords keywords	PROTEIN-DNA COMPLEX, ACTIVE SITE CALCIUM IONS, ALPHA/BETA STRUCTURE, A:A MISMATCH, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1dmu__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1dmu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dmu__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.41 Å
Rg (electron density)	24.37 Å
Total Rg	25.16 Å
Atom count	5428
Residues	632
Excluded volume	94982 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dmu__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(APTPCPGPCPCPTPAPAPTPAPGPGPCPGPAP*T)-3') ;
Molecular weight formula_weight	5211.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F
Atom count atom_count	2969

ATCGCCTAATAGGCGAT

Entity 2 Entity 2 polymer

Description description	BGLI RESTRICTION ENDONUCLEASE
Molecular weight formula_weight	34050.8 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

MYNLHREKIFMSYNQNKQYLEDNPEIQEKIELYGLNLLNEVISDNEEEIRADYNEANFLHPFWMNYPPLDRGKMPKGDQIPWIEVGEKAVGSKLTRLVSQREDITVREIGLPTGPDERYLLTSPTIYSLTNGFTDSIMMFVDIKSVGPRDSDYDLVLSPNQVSGNGDWAQLEGGIQNNQQTIQGPRSSQIFLPTIPPLYILSDGTIAPVVHLFIKPIYAMRSLTKGDTGQSLYKIKLASVPNGLGLFCNPGYAFDSAYKFLFRPGKDDRTKSLLQKRVRVDLRVLDKIGPRVMTIDMDK

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism 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	4

Entity 4 Entity 4 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	255

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dmua_
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.52.1.4 — Restriction endonuclease BglI

CATH v4.4 (1 domains)

Domain ID domain_id	1dmuA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	600 — ECO RV Endonuclease; Chain A
Homologous superfamily homologous superfamily	20 — Restriction endonuclease BglI

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Unit-cell length a length_a	78.480 Å
Unit-cell length b length_b	81.600 Å
Unit-cell length c length_c	117.060 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1830
R_work r_work	0.1770
R_free r_free	0.2390

Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence

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

BGLI RESTRICTION ENDONUCLEASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1dmu__assembly_1__model_1

1dmu__assembly_1__model_1 | I(q)

1dmu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)

Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence

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

BGLI RESTRICTION ENDONUCLEASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1dmu__assembly_1__model_1

1dmu__assembly_1__model_1 | I(q)

1dmu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)