SAXSdb — 1wtd

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

EcoO109IR

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RPJ3_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–272； UniProt 1–272 Author chain B； PDBConstruct 1–272； UniProt 1–272

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	1wtd
Deposition date deposition_date	2004-11-22
Structure title title	Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form
Keywords keywords	RESTRICTION ENDONUCLEASE, DNA-FREE FROM, HYDROLASE; HYDROLASE
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.

1wtd__assembly_1__model_1

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

Download this curve (.dat)

1wtd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wtd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.60 Å
Rg (electron density)	25.17 Å
Total Rg	26.00 Å
Atom count	4185
Residues	531
Excluded volume	74253 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wtd__assembly_1__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	EcoO109IR
Molecular weight formula_weight	31482.0 kDa
EC 编号 ec_number	3.1.21.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4230

MNKQEVILKVQECAAWWILERQSKLTKLMSETMSINPFMTPFIFDYHSLNDFDELVEAIIAKHLMTGHDTGFGKLIDEKILPRVFGAYKLDKSYRAANEPFIHPCFDEIDHVIQRDDGRIELLSLKAGKWTIQLTMAVQLNKAFHEIINNYPGVADNIVVGVFYGNSHGLTDKYRILRGINTGANHNVIDIRDKVHVYAGKEFWSWLNNGEAETQHWVLEGIERAVKEADIKEKNKDLIEKFKEHVAKKYNEQVLNADGTAQWHKLLEMINE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1wtda_
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.52.1.29 — Restriction endonuclease EcoO109IR

Domain ID domain_id	d1wtdb_
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.52.1.29 — Restriction endonuclease EcoO109IR

CATH v4.4 (4 domains)

Domain ID domain_id	1wtdA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3250 — type ii restriction endonuclease, domain 1
Homologous superfamily homologous superfamily	10 — type ii restriction endonuclease, domain 1

Domain ID domain_id	1wtdA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1560 — type ii restriction endonuclease, domain 2
Homologous superfamily homologous superfamily	10 — type ii restriction endonuclease, domain 2

Domain ID domain_id	1wtdB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3250 — type ii restriction endonuclease, domain 1
Homologous superfamily homologous superfamily	10 — type ii restriction endonuclease, domain 1

Domain ID domain_id	1wtdB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1560 — type ii restriction endonuclease, domain 2
Homologous superfamily homologous superfamily	10 — type ii restriction endonuclease, domain 2

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Unit-cell length a length_a	175.551 Å
Unit-cell length b length_b	175.551 Å
Unit-cell length c length_c	44.603 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	16

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.401 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2570
R_work r_work	0.2550
R_free r_free	0.2970

Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form

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

EcoO109IR

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

1wtd__assembly_1__model_1

1wtd__assembly_1__model_1 | I(q)

1wtd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of type II restrcition endonuclease, EcoO109I DNA-free form

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

EcoO109IR

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

1wtd__assembly_1__model_1

1wtd__assembly_1__model_1 | I(q)

1wtd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)