SAXSdb — 3a32

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

Probable threonyl-tRNA synthetase 1

Aeropyrum pernix

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 10 ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYT1_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 1–471

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	3a32
Deposition date deposition_date	2009-06-07
Structure title title	Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix
Keywords keywords	;threonyl-tRNA synthetase, Aeropyrum pernix K1, protein biosynthesis, Aminoacyl-tRNA synthetase, ATP-binding, Ligase, Metal-binding, Nucleotide-binding ;; 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.

3a32__assembly_1__model_1

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

Download this curve (.dat)

3a32__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a32__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.88 Å
Rg (electron density)	28.41 Å
Total Rg	29.32 Å
Atom count	7464
Residues	930
Excluded volume	133500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a32__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 (4)

Entity 1 Entity 1 polymer

Description description	Probable threonyl-tRNA synthetase 1
Molecular weight formula_weight	53194.0 kDa
EC 编号 ec_number	6.1.1.3
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	3966

MASGQDKTHIDYAYELDITVKPDSRVPVFNREFATFTGAGVPLFSLGGGPIRYALAEVLAKFHARRGYYVVETPIIASTELFKVSGHIEFYRNNMYLFDIEGHEFAVKPMNCPYHILLFLNEVAKHRSKLPLPFKVFEFGRVHRYEPSGSIYGLLRVRGFTQDDAHIIVPGGRVIDVVYDVFEEMKLVLERLFKLGVSSETFKVRLSMSDKSLIGKEFMGSKEEWEGAEEALREAASRINEKYGIDIVELEGEAAFYGPKLDFIMMVEESGVSKEWQMGTIQFDFNLPRRFRLYDVVREEFGIEEVYIIHRALLGSIERFLGVYLEHRRGRMPFTLAPIQFAVIAVKTGGEVDREIEDLASSIAKGLLDKGFRVAVKGSSKTGLSSDVRHIESTAKPAVNVFIGAKEVREKVLDVRVFDLESMKRRRLAIAYGDAADAVENLAAVAEELESPVRSLSGQAPRIPADFSFML

Source Source

Source organism organism	Aeropyrum pernix
NCBI taxonomy ID ncbi_taxonomy_id	56636
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	231

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3a32A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	3a32A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

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Unit-cell length a length_a	81.486 Å
Unit-cell length b length_b	103.710 Å
Unit-cell length c length_c	112.537 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	38.300 Å
R factor r_factor	0.1800
R_work r_work	0.1800
R_free r_free	0.2400

Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix

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

Probable threonyl-tRNA synthetase 1

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

3a32__assembly_1__model_1

3a32__assembly_1__model_1 | I(q)

3a32__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix

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

Probable threonyl-tRNA synthetase 1

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

3a32__assembly_1__model_1

3a32__assembly_1__model_1 | I(q)

3a32__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)