SAXSdb — 2hl2

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

Threonyl-tRNA synthetase

Pyrococcus abyssi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYT_PYRAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–143； UniProt 1–143 Author chain B； PDBConstruct 1–143； UniProt 1–143

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	2hl2
Deposition date deposition_date	2006-07-06
Structure title title	Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylate
Keywords keywords	translation, editing, aminoacyl-tRNA synthetase, enzyme mechanism, enantioselectivity, 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.

2hl2__assembly_1__model_1

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

Download this curve (.dat)

2hl2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hl2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.99 Å
Rg (electron density)	18.70 Å
Total Rg	19.74 Å
Atom count	2338
Residues	286
Excluded volume	41895 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hl2__assembly_1__model_1`	dimeric （2）	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	Threonyl-tRNA synthetase
Molecular weight formula_weight	16281.8 kDa
EC 编号 ec_number	6.1.1.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2428

MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNRVYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEE

Source Source

Source organism organism	Pyrococcus abyssi
NCBI taxonomy ID ncbi_taxonomy_id	29292
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
Molecular weight formula_weight	433.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	90

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2hl2a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.110 — DTD-like
Superfamily Superfamily superfamily	c.110.1 — DTD-like
Family Family family	c.110.1.2 — Archaea-specific editing domain of threonyl-tRNA synthetase (Pab-NTD)

Domain ID domain_id	d2hl2b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.110 — DTD-like
Superfamily Superfamily superfamily	c.110.1 — DTD-like
Family Family family	c.110.1.2 — Archaea-specific editing domain of threonyl-tRNA synthetase (Pab-NTD)

CATH v4.4 (2 domains)

Domain ID domain_id	2hl2A01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	10 — D-tyrosyl-tRNA(Tyr) deacylase

Domain ID domain_id	2hl2B01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A;
Homologous superfamily homologous superfamily	10 — D-tyrosyl-tRNA(Tyr) deacylase

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Unit-cell length a length_a	39.652 Å
Unit-cell length b length_b	67.363 Å
Unit-cell length c length_c	98.588 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	24.840 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2950

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylate

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

Threonyl-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

2hl2__assembly_1__model_1

2hl2__assembly_1__model_1 | I(q)

2hl2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylate

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

Threonyl-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

2hl2__assembly_1__model_1

2hl2__assembly_1__model_1 | I(q)

2hl2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)