2nr0

Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA

Method: X-RAY DIFFRACTION

▼

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

tRNA pseudouridine synthase A

Escherichia coli K12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 2 RNA 2	leucyl tRNA × 2	Consistent with all polymers
2	Protein–RNA	Homooligomer	Protein 2 RNA 2	leucyl tRNA × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRUA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 7–270； UniProt 7–270 Author chain B； PDBConstruct 7–270； UniProt 7–270 Author chain C； PDBConstruct 7–270； UniProt 7–270 Author chain D； PDBConstruct 7–270； UniProt 7–270

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2nr0
Deposition date deposition_date	2006-11-01
Structure title title	Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA
Keywords keywords	pseudouridine synthase, anticodon stem loop, tRNA, multisite specificity, ISOMERASE-RNA COMPLEX; ISOMERASE/RNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2nr0__assembly_1__model_1

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

Download this curve (.dat)

2nr0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nr0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.60 Å
Rg (electron density)	31.78 Å
Total Rg	32.55 Å
Atom count	7333
Residues	681
Excluded volume	118500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nr0__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nr0__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	leucyl tRNA
Molecular weight formula_weight	28094.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E,F,G,H
Atom count atom_count	14269

GCCGAGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGGUACCA

Entity 2 Entity 2 polymer

Description description	tRNA pseudouridine synthase A
Molecular weight formula_weight	30441.6 kDa
EC 编号 ec_number	5.4.99.12
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

MSDQQQPPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD

Source Source

Source organism organism	Escherichia coli K12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2nr0a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.265 — Pseudouridine synthase
Superfamily Superfamily superfamily	d.265.1 — Pseudouridine synthase
Family Family family	d.265.1.1 — Pseudouridine synthase I TruA

Domain ID domain_id	d2nr0b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.265 — Pseudouridine synthase
Superfamily Superfamily superfamily	d.265.1 — Pseudouridine synthase
Family Family family	d.265.1.1 — Pseudouridine synthase I TruA

Domain ID domain_id	d2nr0c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.265 — Pseudouridine synthase
Superfamily Superfamily superfamily	d.265.1 — Pseudouridine synthase
Family Family family	d.265.1.1 — Pseudouridine synthase I TruA

Domain ID domain_id	d2nr0d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.265 — Pseudouridine synthase
Superfamily Superfamily superfamily	d.265.1 — Pseudouridine synthase
Family Family family	d.265.1.1 — Pseudouridine synthase I TruA

CATH v4.4 (8 domains)

Domain ID domain_id	2nr0A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	580 — Pseudouridine synthase I, catalytic domain, N-terminal subdomain

Domain ID domain_id	2nr0A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	660 — Pseudouridine synthase I, catalytic domain, C-terminal subdomain

Domain ID domain_id	2nr0B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	580 — Pseudouridine synthase I, catalytic domain, N-terminal subdomain

Domain ID domain_id	2nr0B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	660 — Pseudouridine synthase I, catalytic domain, C-terminal subdomain

Domain ID domain_id	2nr0C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	580 — Pseudouridine synthase I, catalytic domain, N-terminal subdomain

Domain ID domain_id	2nr0C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	660 — Pseudouridine synthase I, catalytic domain, C-terminal subdomain

Domain ID domain_id	2nr0D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	580 — Pseudouridine synthase I, catalytic domain, N-terminal subdomain

Domain ID domain_id	2nr0D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	660 — Pseudouridine synthase I, catalytic domain, C-terminal subdomain

▶

Unit-cell length a length_a	65.033 Å
Unit-cell length b length_b	149.292 Å
Unit-cell length c length_c	291.991 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	3.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2982
R_free r_free	0.3503

Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA

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

tRNA pseudouridine synthase A

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

2nr0__assembly_1__model_1

2nr0__assembly_1__model_1 | I(q)

2nr0__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA

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

tRNA pseudouridine synthase A

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

2nr0__assembly_1__model_1

2nr0__assembly_1__model_1 | I(q)

2nr0__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)