SAXSdb — 3axt

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

Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 SULFATE ION × 8 S-ADENOSYLMETHIONINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRM1_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–392； UniProt 1–392

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	3axt
Deposition date deposition_date	2011-04-14
Structure title title	Complex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with S-adenosyl-L-Methionine
Keywords keywords	;Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, tRNA modification enzyme, guanine 26, N2, N2-dimethyltransferase, Aquifex aeolicus, TRANSFERASE ;; TRANSFERASE
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.

3axt__assembly_1__model_1

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

Download this curve (.dat)

3axt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3axt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.68 Å
Rg (electron density)	29.99 Å
Total Rg	30.74 Å
Atom count	6420
Residues	774
Excluded volume	115910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3axt__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 (5)

Entity 1 Entity 1 polymer

Description description	Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1
Molecular weight formula_weight	45548.2 kDa
EC 编号 ec_number	2.1.1.32
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	3270

MEIVQEGIAKIIVPEIPKTVSSDMPVFYNPRMRVNRDLAVLGLEYLCKKLGRPVKVADPLSASGIRAIRFLLETSCVEKAYANDISSKAIEIMKENFKLNNIPEDRYEIHGMEANFFLRKEWGFGFDYVDLDPFGTPVPFIESVALSMKRGGILSLTATDTAPLSGTYPKTCMRRYMARPLRNEFKHEVGIRILIKKVIELAAQYDIAMIPIFAYSHLHYFKLFFVKERGVEKVDKLIEQFGYIQYCFNCMNREVVTDLYKFKEKCPHCGSKFHIGGPLWIGKLWDEEFTNFLYEEAQKREEIEKETKRILKLIKEESQLQTVGFYVLSKLAEKVKLPAQPPIRIAVKFFNGVRTHFVGDGFRTNLSFEEVMKKMEELKEKQKEFLEKKKQG

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
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	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	4

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	53

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3axtA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3axtA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	70 — N2,N2-dimethylguanosine tRNA methyltransferase, C-terminal domain

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Unit-cell length a length_a	54.438 Å
Unit-cell length b length_b	140.928 Å
Unit-cell length c length_c	119.038 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	2.491 Å
Low-resolution limit resolution_low	27.415 Å
R factor r_factor	0.1871
R_work r_work	0.1853
R_free r_free	0.2246

Complex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with S-adenosyl-L-Methionine

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

Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1

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

3axt__assembly_1__model_1

3axt__assembly_1__model_1 | I(q)

3axt__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Complex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with S-adenosyl-L-Methionine

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

Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1

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

3axt__assembly_1__model_1

3axt__assembly_1__model_1 | I(q)

3axt__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)