SAXSdb — 1wnz

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

isoleucyl-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	2'-(L-VALYL)AMINO-2'-DEOXYADENOSINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYI_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–186； UniProt 201–385

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	1wnz
Deposition date deposition_date	2004-08-11
Structure title title	Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA
Keywords keywords	;Ligase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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.

1wnz__assembly_1__model_1

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

Download this curve (.dat)

1wnz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wnz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.95 Å
Rg (electron density)	15.69 Å
Total Rg	16.86 Å
Atom count	1433
Residues	180
Excluded volume	25812 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wnz__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	isoleucyl-trna synthetase
Molecular weight formula_weight	20629.6 kDa
EC 编号 ec_number	6.1.1.5
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	1616

MQDPSVYVRFPLKEPKKLGLEKASLLIWTTTPWTLPGNVAAAVHPEYTYAAFQVGDEALILEEGLGRKLLGEGTPVLKTFPGKALEGLPYTPPYPQALEKGYFVVLADYVSQEDGTGIVHQAPAFGAEDLETARVYGLPLLKTVDEEGKLLVEPFKGLYFREANRAILRDLRGRGLLFKEESYLHS

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	2'-(L-VALYL)AMINO-2'-DEOXYADENOSINE
Molecular weight formula_weight	365.4 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	183

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1wnza_
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	1wnzA00
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	72.594 Å
Unit-cell length b length_b	72.594 Å
Unit-cell length c length_c	83.683 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 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	33.300 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2570

Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA

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

isoleucyl-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

1wnz__assembly_1__model_1

1wnz__assembly_1__model_1 | I(q)

1wnz__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)

Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA

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

isoleucyl-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

1wnz__assembly_1__model_1

1wnz__assembly_1__model_1 | I(q)

1wnz__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)