SAXSdb — 3ebc

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

Type-2 restriction enzyme HincII

Haemophilus influenzae

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	5'-D(DGPDCPDCPDGPDGPDTPDCPDGPDAPDCPDGPDGPDGPDC)-3' × 1 5'-D(DGPDCPDCPDCPDGPDTPDCPDGPDAPDCPDCPDGPDGPDC)-3' × 1 MANGANESE (II) ION × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	T2C2_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–260； UniProt 1–258 Author chain B； PDBConstruct 3–260； UniProt 1–258

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	3ebc
Deposition date deposition_date	2008-08-27
Structure title title	Structure of N141A HincII with Cognate DNA
Keywords keywords	intermediate, mutant, dimerization, R-loop, Endonuclease, Hydrolase, Nuclease, Restriction system, 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.

3ebc__assembly_1__model_1

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

Download this curve (.dat)

3ebc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ebc__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)	24.48 Å
Total Rg	25.23 Å
Atom count	4458
Residues	513
Excluded volume	77967 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ebc__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	Type-2 restriction enzyme HincII
Molecular weight formula_weight	36593.5 kDa
EC 编号 ec_number	3.1.21.4
Mutation mutation	N141A
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	4759

MAMSFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPAIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYILRSRELVDPNSVQARLQDVDGTIDTRSKLAAAQLYTRASQPELAPEDPEDLEHHHHHH

Source Source

Source organism organism	Haemophilus influenzae
NCBI taxonomy ID ncbi_taxonomy_id	727
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(DGPDCPDCPDGPDGPDTPDCPDGPDAPDCPDGPDGPDGPDC)-3'
Molecular weight formula_weight	4322.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

GCCGGTCGACGGGC

Entity 3 Entity 3 polymer

Description description	5'-D(DGPDCPDCPDCPDGPDTPDCPDGPDAPDCPDCPDGPDGPDC)-3'
Molecular weight formula_weight	4242.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

GCCCGTCGACCGGC

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 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	301

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ebca_
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.52.1.19 — Restriction endonuclease HincII

Domain ID domain_id	d3ebcb_
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.52.1.19 — Restriction endonuclease HincII

CATH v4.4 (2 domains)

Domain ID domain_id	3ebcA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	600 — ECO RV Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — DNA mismatch repair MutH/Restriction endonuclease, type II

Domain ID domain_id	3ebcB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	600 — ECO RV Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — DNA mismatch repair MutH/Restriction endonuclease, type II

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Unit-cell length a length_a	46.551 Å
Unit-cell length b length_b	91.571 Å
Unit-cell length c length_c	70.594 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	43.560 Å
R factor r_factor	0.1950
R_work r_work	0.1910
R_free r_free	0.2790

Structure of N141A HincII with Cognate DNA

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

Type-2 restriction enzyme HincII

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

3ebc__assembly_1__model_1

3ebc__assembly_1__model_1 | I(q)

3ebc__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of N141A HincII with Cognate DNA

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

Type-2 restriction enzyme HincII

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

3ebc__assembly_1__model_1

3ebc__assembly_1__model_1 | I(q)

3ebc__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)