6ozf

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

Method: X-RAY DIFFRACTION

▼

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

Endonuclease V

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA/RNA (5'-D(PAPAPTPGPI)-R(PA)-D(PGPAPTPGPCPT)-3') ; × 1 CALCIUM ION × 2 SODIUM ION × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA/RNA (5'-D(PAPAPTPGPI)-R(PA)-D(PGPAPTPGPCPT)-3') ; × 1 CALCIUM ION × 2 SODIUM ION × 1 GLYCEROL × 2 1,2-ETHANEDIOL × 1 TETRAETHYLENE GLYCOL × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NFI_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–225； UniProt 1–225 Author chain B； PDBConstruct 1–225； UniProt 1–225

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6ozf
Deposition date deposition_date	2019-05-15
Structure title title	Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine
Keywords keywords	Nucleic acid hydrolysis, RNA recognition, metal ion dependent catalysis, DNA damage, adenosine deamination, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6ozf__assembly_1__model_1

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

Download this curve (.dat)

6ozf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ozf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.29 Å
Rg (electron density)	17.03 Å
Total Rg	18.10 Å
Atom count	1997
Residues	232
Excluded volume	35421 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ozf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ozf__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Endonuclease V
Molecular weight formula_weight	25635.0 kDa
EC 编号 ec_number	3.1.21.7
Mutation mutation	D110N
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	4478

MDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFNGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLKKGLF

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA/RNA (5'-D(PAPAPTPGPI)-R(PA)-D(PGPAPTPGPCPT)-3') ;
Molecular weight formula_weight	3727.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide/polyribonucleotide hybrid
Chain IDs strand_id	C,D

AATGIAGATGCT

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	330

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6ozfA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2170 — archaeoglobus fulgidus dsm 4304 fold
Homologous superfamily homologous superfamily	10 — archaeoglobus fulgidus dsm 4304 superfamily

Domain ID domain_id	6ozfB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2170 — archaeoglobus fulgidus dsm 4304 fold
Homologous superfamily homologous superfamily	10 — archaeoglobus fulgidus dsm 4304 superfamily

▶

Unit-cell length a length_a	63.129 Å
Unit-cell length b length_b	75.578 Å
Unit-cell length c length_c	106.397 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	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	28.093 Å
R factor r_factor	0.1685
R_work r_work	0.1670
R_free r_free	0.1977

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

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

Endonuclease V

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

6ozf__assembly_1__model_1

6ozf__assembly_1__model_1 | I(q)

6ozf__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

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

Endonuclease V

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

6ozf__assembly_1__model_1

6ozf__assembly_1__model_1 | I(q)

6ozf__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)