1a79

CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOCOCCUS JANNASCHII

Method: X-RAY DIFFRACTION

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

TRNA ENDONUCLEASE

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 2 GOLD ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENDA_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–171； UniProt 9–179 Author chain B； PDBConstruct 1–171； UniProt 9–179 Author chain C； PDBConstruct 1–171； UniProt 9–179 Author chain D； PDBConstruct 1–171； UniProt 9–179

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	1a79
Deposition date deposition_date	1998-03-23
Structure title title	CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOCOCCUS JANNASCHII
Keywords keywords	ENDONUCLEASE, TRNA ENDONUCLEASE; ENDONUCLEASE
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.

1a79__assembly_1__model_1

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

Download this curve (.dat)

1a79__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1a79__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.17 Å
Rg (electron density)	31.05 Å
Total Rg	31.37 Å
Atom count	5598
Residues	684
Excluded volume	101160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1a79__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 (4)

Entity 1 Entity 1 polymer

Description description	TRNA ENDONUCLEASE
Molecular weight formula_weight	19745.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5651

KITGLLDGDRVIVFDKNGISKLSARHYGNVEGNFLSLSLVEALYLINLGWLEVKYKDNKPLSFEELYEYARNVEERLCLKYLVYKDLRTRGYIVKTGLKYGADFRLYERGANIDKEHSVYLVKVFPEDSSFLLSELTGFVRVAHSVRKKLLIAIVDADGDIVYYNMTYVKP

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GOLD ION
Molecular weight formula_weight	197.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	53

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1a79a1
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	d1a79a2
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	d1a79b1
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	d1a79b2
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	d1a79c1
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	d1a79c2
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	d1a79d1
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	d1a79d2
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 (8 domains)

Domain ID domain_id	1a79A01
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	1a79A02
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	1a79B01
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	1a79B02
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	1a79C01
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	1a79C02
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	1a79D01
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	1a79D02
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

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Unit-cell length a length_a	61.950 Å
Unit-cell length b length_b	80.040 Å
Unit-cell length c length_c	193.590 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2670

CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOCOCCUS JANNASCHII

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

TRNA 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

1a79__assembly_1__model_1

1a79__assembly_1__model_1 | I(q)

1a79__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOCOCCUS JANNASCHII

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

TRNA 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

1a79__assembly_1__model_1

1a79__assembly_1__model_1 | I(q)

1a79__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)