SAXSdb — 1iyw

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

Valyl-tRNA Synthetase

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYV_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–862； UniProt 1–862 Author chain B； PDBConstruct 1–862； UniProt 1–862

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	1iyw
Deposition date deposition_date	2002-09-10
Structure title title	Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase
Keywords keywords	Rossmann Fold, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, LIGASE; LIGASE
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.

1iyw__assembly_2__model_1

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

Download this curve (.dat)

1iyw__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1iyw__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	36.93 Å
Rg (electron density)	36.78 Å
Total Rg	36.81 Å
Atom count	0
Residues	0
Excluded volume	121300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1iyw__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1iyw__assembly_2__model_1`	monomeric （1）	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 (1)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1iywa1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.7 — tRNA-binding arm
Family Family family	a.2.7.3 — Valyl-tRNA synthetase (ValRS) C-terminal domain

Domain ID domain_id	d1iywa2
Class class	a — All alpha proteins
Fold Fold fold	a.27 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily Superfamily superfamily	a.27.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family Family family	a.27.1.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases

Domain ID domain_id	d1iywa3
Class class	b — All beta proteins
Fold Fold fold	b.51 — ValRS/IleRS/LeuRS editing domain
Superfamily Superfamily superfamily	b.51.1 — ValRS/IleRS/LeuRS editing domain
Family Family family	b.51.1.1 — ValRS/IleRS/LeuRS editing domain

Domain ID domain_id	d1iywa4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Domain ID domain_id	d1iywb1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.7 — tRNA-binding arm
Family Family family	a.2.7.3 — Valyl-tRNA synthetase (ValRS) C-terminal domain

Domain ID domain_id	d1iywb2
Class class	a — All alpha proteins
Fold Fold fold	a.27 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily Superfamily superfamily	a.27.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family Family family	a.27.1.1 — Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases

Domain ID domain_id	d1iywb3
Class class	b — All beta proteins
Fold Fold fold	b.51 — ValRS/IleRS/LeuRS editing domain
Superfamily Superfamily superfamily	b.51.1 — ValRS/IleRS/LeuRS editing domain
Family Family family	b.51.1.1 — ValRS/IleRS/LeuRS editing domain

Domain ID domain_id	d1iywb4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

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Unit-cell length a length_a	186.562 Å
Unit-cell length b length_b	207.328 Å
Unit-cell length c length_c	59.235 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	4.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.3196
R_work r_work	0.3164
R_free r_free	0.3828

Description description	Valyl-tRNA Synthetase
Molecular weight formula_weight	98914.4 kDa
EC 编号 ec_number	6.1.1.9
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1724

Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase

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

Valyl-tRNA Synthetase

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

1iyw__assembly_2__model_1

1iyw__assembly_2__model_1 | I(q)

1iyw__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli

Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase

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

Valyl-tRNA Synthetase

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

1iyw__assembly_2__model_1

1iyw__assembly_2__model_1 | I(q)

1iyw__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)