SAXSdb — 1wk9

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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	5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE × 1 water × 1	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 2–146； UniProt 193–337

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	1wk9
Deposition date deposition_date	2004-05-30
Structure title title	Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain
Keywords keywords	;editing, cp1, valyl-trna synthetase, fidelity, thermus thrmophilus, translation, amino acid, thr-ams, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

1wk9__assembly_1__model_1

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

Download this curve (.dat)

1wk9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wk9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.88 Å
Rg (electron density)	14.50 Å
Total Rg	15.64 Å
Atom count	1175
Residues	143
Excluded volume	20768 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wk9__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Valyl-tRNA synthetase
Molecular weight formula_weight	16540.8 kDa
EC 编号 ec_number	6.1.1.9
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1351

MTPGKLYTLRYEVEGGGFIEIATVRPETVFADQAIAVHPEDERYRHLLGKRARIPLTEVWIPILADPAVEKDFGTGALKVTPAHDPLDYEIGERHGLKPVSVINLEGRMEGERVPEALRGLDRFEARRKAVELFREAGHLVKEEDY

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE
Molecular weight formula_weight	447.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1wk9a_
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

CATH v4.4 (1 domains)

Domain ID domain_id	1wk9A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	740 — Isoleucyl-tRNA Synthetase; domain 2
Homologous superfamily homologous superfamily	10 — Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain

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Unit-cell length a length_a	95.490 Å
Unit-cell length b length_b	95.490 Å
Unit-cell length c length_c	72.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	47.750 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2470

Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain

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

1wk9__assembly_1__model_1

1wk9__assembly_1__model_1 | I(q)

1wk9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain

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

1wk9__assembly_1__model_1

1wk9__assembly_1__model_1 | I(q)

1wk9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)