SAXSdb — 6n67

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

tRNA ligase

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 SULFATE ION × 2 CHLORIDE ION × 3 GLYCEROL × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0S6G2_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–434； UniProt 2–414

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	6n67
Deposition date deposition_date	2018-11-26
Structure title title	Crystal structure of the ligase domain of fungal tRNA ligase Trl1
Keywords keywords	RNA ligase, tRNA splicing, inhibitor, ATP-binding, 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.

6n67__assembly_1__model_1

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

Download this curve (.dat)

6n67__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6n67__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.80 Å
Rg (electron density)	21.88 Å
Total Rg	22.84 Å
Atom count	3181
Residues	386
Excluded volume	56289 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6n67__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 (6)

Entity 1 Entity 1 polymer

Description description	tRNA ligase
Molecular weight formula_weight	49061.5 kDa
EC 编号 ec_number	6.5.1.3
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	3457

MGSSHHHHHHSSGLVPRGSHMDGTAEKQRDSLASRYKASTDYAKDAEGLTAPYVSQDPQETAALVRALDDAAKKGKKSGGFSVKKTRYAVASSPTGAEVDSWRFNDWDYKKPDLPTYARGLFTTRTQHGVPEIAVRGYDKFFNIDETRDTAWSAIRERTKGPYELTLKENGCIIFISGLEDGTLLVCSKHSTGDRSDVALSHSSAGEKHLEAQLERIGKTKEELARELRKRNATAVAELCDDSFEEHILAYGPDKAGLYLHGINLNIPEFITYPSPLVQKFAEDWGFRKTGLIIIDNIDDVKAFLEEVAETGAHDGRDVEGFVIRCKKSTNPGVGPYHDWFFKYKFEEPYLMYRQWRECTKALISGKQPKIKKHVKITEEYLLYARKRLAADPKLAKLYNQNHGIIKLRNDFLEYKNMKGTDAANLEDDGAASV

Source Source

Source organism organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	276

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Unit-cell length a length_a	49.729 Å
Unit-cell length b length_b	56.580 Å
Unit-cell length c length_c	173.879 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	37.740 Å
R factor r_factor	0.1717
R_work r_work	0.1695
R_free r_free	0.2144

Crystal structure of the ligase domain of fungal tRNA ligase Trl1

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

tRNA ligase

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

6n67__assembly_1__model_1

6n67__assembly_1__model_1 | I(q)

6n67__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of the ligase domain of fungal tRNA ligase Trl1

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

tRNA ligase

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

6n67__assembly_1__model_1

6n67__assembly_1__model_1 | I(q)

6n67__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)