1a79

CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOCOCCUS JANNASCHII

Method: X-RAY DIFFRACTION D_max: 114.3 Å Quality: GOOD

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

TRNA ENDONUCLEASE

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 9–179 Chain B； UniProt 9–179 Chain C； UniProt 9–179 Chain D； UniProt 9–179	Not recorded	SO4 SULFATE ION × 2 AU GOLD ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.28 Å R-free 0.267

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.17 Å
Radius of gyration Rg (electron density) rg_electron	31.05 Å
Forward intensity I(0) i0	92830500.00
Molecular weight molecular_weight	79859.0 kDa
Excluded volume excluded_volume	101160 Å³
Envelope volume envelope_volume	120490 Å³
Hydration-shell volume shell_volume	33976 Å³
Envelope diameter envelope_diameter	118.1 Å
Shell Rg shell_rg	36.15 Å
Envelope Rg envelope_rg	31.41 Å
Shape Rg shape_rg	31.08 Å
Total Rg total_rg	31.37 Å
Total atoms total_atoms	5598
Residues n_residues	684
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	114.3 Å
Rg (real space) rg_real	31.42 Å
Rg uncertainty (real space) rg_real_error	1.16 Å
I(0) (real space) i0_real	9.2830e+07
I(0) uncertainty (real space) i0_real_error	1.7160e+06
Rg (reciprocal space) rg_reciprocal	31.31 Å
I(0) (reciprocal space) i0_reciprocal	92820000.0000
Solution quality estimate total_estimate	0.8105
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.4 Å
Skewness Skewness skewness	0.582
Kurtosis Kurtosis kurtosis	-0.012
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38920000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.646; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.687; Smooth: 0.907

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Methanocaldococcus jannaschii
NCBI Class编号 ncbi_taxonomy_id	2190
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/a7/1a79/1a79.fit
pddf	/app/data/pr_computation/a7/1a79/1a79.pr.out
profile	/app/data/saxs_computation/a7/1a79/1a79.dat