1r0v

Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21212 space group

Method: X-RAY DIFFRACTION

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

tRNA-intron endonuclease

Archaeoglobus fulgidus

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	ENDA_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–305； UniProt 1–305 Author chain B； PDBConstruct 1–305； UniProt 1–305 Author chain C； PDBConstruct 1–305； UniProt 1–305 Author chain D； PDBConstruct 1–305； UniProt 1–305

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	1r0v
Deposition date deposition_date	2003-09-23
Structure title title	Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21212 space group
Keywords keywords	RNA splicing; endonuclease; x-ray crystallography, TRANSLATION, HYDROLASE; TRANSLATION, 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.

1r0v__assembly_1__model_1

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

Download this curve (.dat)

1r0v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1r0v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.78 Å
Rg (electron density)	24.94 Å
Total Rg	25.83 Å
Atom count	4100
Residues	488
Excluded volume	73260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1r0v__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1r0v__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) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1r0va1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d1r0va2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d1r0va3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d1r0vb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d1r0vb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d1r0vb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d1r0vc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d1r0vc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d1r0vc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

Domain ID domain_id	d1r0vd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d1r0vd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
Family Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

Domain ID domain_id	d1r0vd3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.75 — MutS N-terminal domain-like
Superfamily Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
Family Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

CATH v4.4 (12 domains)

Domain ID domain_id	1r0vA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1r0vA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

Domain ID domain_id	1r0vA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1r0vB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1r0vB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

Domain ID domain_id	1r0vB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1r0vC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1r0vC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

Domain ID domain_id	1r0vC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1r0vD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1r0vD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

Domain ID domain_id	1r0vD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	128.119 Å
Unit-cell length b length_b	144.149 Å
Unit-cell length c length_c	52.385 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	95.350 Å
R factor r_factor	0.1771
R_work r_work	0.1736
R_free r_free	0.2420

Description description	tRNA-intron endonuclease
Molecular weight formula_weight	36000.2 kDa
EC 编号 ec_number	3.1.27.9
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9073

Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21212 space group

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

tRNA-intron endonuclease

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

1r0v__assembly_1__model_1

1r0v__assembly_1__model_1 | I(q)

1r0v__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	224325
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	881

Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21212 space group

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

tRNA-intron endonuclease

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

1r0v__assembly_1__model_1

1r0v__assembly_1__model_1 | I(q)

1r0v__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)