SAXSdb — 3e43

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

Type-2 restriction enzyme HindII

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(DGPDCPDCPDGPDGPDTPDTPDAPDAPDCPDCPDGPDGPDC)-3' × 2 UNKNOWN ATOM OR ION × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	T2D2_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–257； UniProt 2–258 Author chain B； PDBConstruct 1–257； UniProt 2–258

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	3e43
Deposition date deposition_date	2008-08-08
Structure title title	Q138F HincII bound to GTTAAC and cocrystallized with 2.5 mM MgCl2
Keywords keywords	protein-DNA complex, endonuclease, indirect readout, 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.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e43__assembly_1__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Type-2 restriction enzyme HindII
Molecular weight formula_weight	29839.1 kDa
EC 编号 ec_number	3.1.21.4
Mutation mutation	Q138F
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	4538

SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAFAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL

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(DGPDCPDCPDGPDGPDTPDTPDAPDAPDCPDCPDGPDGPDC)-3'
Molecular weight formula_weight	4281.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F

GCCGGTTAACCGGC

Entity 3 Entity 3 non-polymer

Description description	UNKNOWN ATOM OR ION
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	106

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3e43a_
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	d3e43b_
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	3e43A00
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	3e43B00
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	50.271 Å
Unit-cell length b length_b	90.938 Å
Unit-cell length c length_c	66.526 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.14 °
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	2.730 Å
Low-resolution limit resolution_low	44.741 Å
R factor r_factor	0.1960
R_work r_work	0.1920
R_free r_free	0.2750

Q138F HincII bound to GTTAAC and cocrystallized with 2.5 mM MgCl2

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

Type-2 restriction enzyme HindII

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Q138F HincII bound to GTTAAC and cocrystallized with 2.5 mM MgCl2

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

Type-2 restriction enzyme HindII

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

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)