3exa

Crystal structure of the full-length tRNA isopentenylpyrophosphate transferase (BH2366) from Bacillus halodurans, Northeast Structural Genomics Consortium target BhR41.

Method: X-RAY DIFFRACTION

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

tRNA delta(2)-isopentenylpyrophosphate transferase

Bacillus halodurans

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	MIAA_BACHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–314； UniProt 1–314 Author chain B； PDBConstruct 1–314； UniProt 1–314 Author chain C； PDBConstruct 1–314； UniProt 1–314 Author chain D； PDBConstruct 1–314； UniProt 1–314

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	3exa
Deposition date deposition_date	2008-10-16
Structure title title	Crystal structure of the full-length tRNA isopentenylpyrophosphate transferase (BH2366) from Bacillus halodurans, Northeast Structural Genomics Consortium target BhR41.
Keywords keywords	;alpha-beta protein, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, ATP-binding, Nucleotide-binding, Nucleotidyltransferase, Transferase, tRNA processing ;; TRANSFERASE
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.

3exa__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3exa__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3exa__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.42 Å
Rg (electron density)	35.05 Å
Total Rg	35.77 Å
Atom count	4842
Residues	585
Excluded volume	86481 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3exa__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3exa__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) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3exaa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.26 — Adenosine phosphateisopentenyltransferase (IPT)-like

Domain ID domain_id	d3exaa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3exab1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.26 — Adenosine phosphateisopentenyltransferase (IPT)-like

Domain ID domain_id	d3exab2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3exac1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.26 — Adenosine phosphateisopentenyltransferase (IPT)-like

Domain ID domain_id	d3exac2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3exad1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.26 — Adenosine phosphateisopentenyltransferase (IPT)-like

Domain ID domain_id	d3exad2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	3exaA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3exaA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	890 — Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain

Domain ID domain_id	3exaB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3exaB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	890 — Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain

Domain ID domain_id	3exaC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3exaC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	890 — Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain

Domain ID domain_id	3exaD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3exaD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	890 — Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain

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Unit-cell length a length_a	51.805 Å
Unit-cell length b length_b	73.824 Å
Unit-cell length c length_c	95.561 Å
Unit-cell angle α angle_alpha	89.99 °
Unit-cell angle β angle_beta	93.73 °
Unit-cell angle γ angle_gamma	90.02 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2630

Description description	tRNA delta(2)-isopentenylpyrophosphate transferase
Molecular weight formula_weight	37402.8 kDa
EC 编号 ec_number	2.5.1.8
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	10249

Crystal structure of the full-length tRNA isopentenylpyrophosphate transferase (BH2366) from Bacillus halodurans, Northeast Structural Genomics Consortium target BhR41.

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

tRNA delta(2)-isopentenylpyrophosphate transferase

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

3exa__assembly_2__model_1

3exa__assembly_2__model_1 | I(q)

3exa__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Bacillus halodurans
NCBI taxonomy ID ncbi_taxonomy_id	86665
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	565

Crystal structure of the full-length tRNA isopentenylpyrophosphate transferase (BH2366) from Bacillus halodurans, Northeast Structural Genomics Consortium target BhR41.

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

tRNA delta(2)-isopentenylpyrophosphate transferase

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

3exa__assembly_2__model_1

3exa__assembly_2__model_1 | I(q)

3exa__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)