3p1y

Crystal structure of the chimeric Archaeoglobus fulgidus RNA splicing endonuclease with the broadest substrate specificity

Method: X-RAY DIFFRACTION

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

tRNA-splicing endonuclease

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Insufficient information	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 2–173； UniProt 2–173 Author chain A； PDBConstruct 189–315； UniProt 179–305 Author chain B； PDBConstruct 2–173； UniProt 2–173 Author chain B； PDBConstruct 189–315； UniProt 179–305 Author chain C； PDBConstruct 2–173； UniProt 2–173 Author chain C； PDBConstruct 189–315； UniProt 179–305 Author chain D； PDBConstruct 2–173； UniProt 2–173 Author chain D； PDBConstruct 189–315； UniProt 179–305

tRNA-splicing endonuclease

Archaeoglobus fulgidus

UniProt Q9YBF1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Insufficient information	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_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 174–188； UniProt 39–53 Author chain B； PDBConstruct 174–188； UniProt 39–53 Author chain C； PDBConstruct 174–188； UniProt 39–53 Author chain D； PDBConstruct 174–188； UniProt 39–53

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	3p1y
Deposition date deposition_date	2010-10-01
Structure title title	Crystal structure of the chimeric Archaeoglobus fulgidus RNA splicing endonuclease with the broadest substrate specificity
Keywords keywords	Protein homodimer, RNA splicing endonuclease, broad substrate specificity, HYDROLASE; 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.

3p1y__assembly_1__model_1

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

Download this curve (.dat)

3p1y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3p1y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.35 Å
Rg (electron density)	28.98 Å
Total Rg	29.62 Å
Atom count	5212
Residues	628
Excluded volume	93217 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3p1y__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3p1y__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) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3p1yA01
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	150 —

Domain ID domain_id	3p1yA02
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	3p1yA03
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	3p1yB01
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	150 —

Domain ID domain_id	3p1yB02
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	3p1yB03
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	3p1yC01
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	150 —

Domain ID domain_id	3p1yC02
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	3p1yC03
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	3p1yD01
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	150 —

Domain ID domain_id	3p1yD02
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	3p1yD03
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	81.770 Å
Unit-cell length b length_b	104.642 Å
Unit-cell length c length_c	165.303 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	2.050 Å
Low-resolution limit resolution_low	38.890 Å
R factor r_factor	0.2498
R_work r_work	0.2471
R_free r_free	0.2867

Description description	tRNA-splicing endonuclease
Molecular weight formula_weight	37081.4 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	10726

Crystal structure of the chimeric Archaeoglobus fulgidus RNA splicing endonuclease with the broadest substrate specificity

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

tRNA-splicing endonuclease

State in the Current Structure

Other States of the Same Protein in the Database

tRNA-splicing 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

3p1y__assembly_1__model_1

3p1y__assembly_1__model_1 | I(q)

3p1y__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
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	302

Crystal structure of the chimeric Archaeoglobus fulgidus RNA splicing endonuclease with the broadest substrate specificity

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

tRNA-splicing 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

tRNA-splicing 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

3p1y__assembly_1__model_1

3p1y__assembly_1__model_1 | I(q)

3p1y__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)