SAXSdb — 1wxo

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

alanyl-tRNA synthetase

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O58307_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–157； UniProt 1–157 Author chain B； PDBConstruct 1–157； UniProt 1–157 Author chain C； PDBConstruct 1–157； UniProt 1–157

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	1wxo
Deposition date deposition_date	2005-01-27
Structure title title	Structure of Archaeal Trans-Editing Protein AlaX in complex with zinc
Keywords keywords	HYDROLASE, Trans-editing; HYDROLASE
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.

1wxo__assembly_2__model_1

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

Download this curve (.dat)

1wxo__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wxo__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	16.52 Å
Rg (electron density)	15.37 Å
Total Rg	16.54 Å
Atom count	1258
Residues	154
Excluded volume	22720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wxo__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wxo__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1wxo__assembly_3__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	alanyl-tRNA synthetase
Molecular weight formula_weight	18183.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4162

MYSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLELENPS

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	422

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1wxoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.67 — RRF/tRNA synthetase additional domain-like
Superfamily Superfamily superfamily	d.67.1 — ThrRS/AlaRS common domain
Family Family family	d.67.1.2 — AlaX-like

Domain ID domain_id	d1wxob_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.67 — RRF/tRNA synthetase additional domain-like
Superfamily Superfamily superfamily	d.67.1 — ThrRS/AlaRS common domain
Family Family family	d.67.1.2 — AlaX-like

Domain ID domain_id	d1wxoc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.67 — RRF/tRNA synthetase additional domain-like
Superfamily Superfamily superfamily	d.67.1 — ThrRS/AlaRS common domain
Family Family family	d.67.1.2 — AlaX-like

CATH v4.4 (6 domains)

Domain ID domain_id	1wxoA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	980 — Threonyl-tRNA Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Threonyl-trna Synthetase; Chain A, domain 2

Domain ID domain_id	1wxoA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	54 — Replication Terminator Protein; Chain A, domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1wxoB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	980 — Threonyl-tRNA Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Threonyl-trna Synthetase; Chain A, domain 2

Domain ID domain_id	1wxoB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	54 — Replication Terminator Protein; Chain A, domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1wxoC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	980 — Threonyl-tRNA Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Threonyl-trna Synthetase; Chain A, domain 2

Domain ID domain_id	1wxoC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	54 — Replication Terminator Protein; Chain A, domain 2
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	42.472 Å
Unit-cell length b length_b	97.971 Å
Unit-cell length c length_c	60.584 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.81 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.1926
R_free r_free	0.2318

Structure of Archaeal Trans-Editing Protein AlaX in complex with zinc

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

alanyl-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

1wxo__assembly_2__model_1

1wxo__assembly_2__model_1 | I(q)

1wxo__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 (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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of Archaeal Trans-Editing Protein AlaX in complex with zinc

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

alanyl-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

1wxo__assembly_2__model_1

1wxo__assembly_2__model_1 | I(q)

1wxo__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 (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) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)