SAXSdb — 1ni0

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

Type II restriction enzyme PvuII

Proteus vulgaris

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	T2P2_PROVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–157； UniProt 1–157 Author chain B； PDBConstruct 1–157； UniProt 1–157 Author chain C； PDBConstruct 1–157； UniProt 1–157

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	1ni0
Deposition date deposition_date	2002-12-20
Structure title title	Structure of the Y94F mutant of the restriction endonuclease PvuII
Keywords keywords	Restriction endonuclease, PvuII, Point mutation, 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.

1ni0__assembly_1__model_1

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

Download this curve (.dat)

1ni0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ni0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.68 Å
Rg (electron density)	24.09 Å
Total Rg	24.82 Å
Atom count	2590
Residues	314
Excluded volume	46294 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ni0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ni0__assembly_2__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 (2)

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1ni0a1
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.52.1.6 — Restriction endonuclease PvuII

Domain ID domain_id	d1ni0a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ni0b1
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.52.1.6 — Restriction endonuclease PvuII

Domain ID domain_id	d1ni0b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ni0c1
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.52.1.6 — Restriction endonuclease PvuII

Domain ID domain_id	d1ni0c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	1ni0A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	210 — PvuII Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — PVUII Endonuclease, subunit A

Domain ID domain_id	1ni0B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	210 — PvuII Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — PVUII Endonuclease, subunit A

Domain ID domain_id	1ni0C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	210 — PvuII Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — PVUII Endonuclease, subunit A

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Unit-cell length a length_a	176.860 Å
Unit-cell length b length_b	176.860 Å
Unit-cell length c length_c	46.340 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	24

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2900

Description description	Type II restriction enzyme PvuII
Molecular weight formula_weight	18497.1 kDa
EC 编号 ec_number	3.1.21.4
Mutation mutation	Y94F
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4078

Structure of the Y94F mutant of the restriction endonuclease PvuII

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

Type II restriction enzyme PvuII

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

1ni0__assembly_1__model_1

1ni0__assembly_1__model_1 | I(q)

1ni0__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Source organism organism	Proteus vulgaris
NCBI taxonomy ID ncbi_taxonomy_id	585
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

Structure of the Y94F mutant of the restriction endonuclease PvuII

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

Type II restriction enzyme PvuII

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

1ni0__assembly_1__model_1

1ni0__assembly_1__model_1 | I(q)

1ni0__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)