SAXSdb — 2eju

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

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

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	S-ADENOSYL-L-HOMOCYSTEINE × 1 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRM1_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–378； UniProt 4–381

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	2eju
Deposition date deposition_date	2007-03-20
Structure title title	Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein
Keywords keywords	;tRNA modification enzyme, guanine-26, N(2)-N(2)-dimethyltransferase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

2eju__assembly_1__model_1

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

Download this curve (.dat)

2eju__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2eju__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.76 Å
Rg (electron density)	21.75 Å
Total Rg	22.68 Å
Atom count	2998
Residues	371
Excluded volume	54010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2eju__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2eju__assembly_2__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	N(2),N(2)-dimethylguanosine tRNA methyltransferase
Molecular weight formula_weight	43010.9 kDa
EC 编号 ec_number	2.1.1.32
Mutation mutation	L1M
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	3334

MELIEVQEGKAKILIPKAESIYDSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRRLKIETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIKRI

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	336

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2ejua_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.58 — TRM1-like

CATH v4.4 (2 domains)

Domain ID domain_id	2ejuA01
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	2ejuA02
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	74.781 Å
Unit-cell length b length_b	109.655 Å
Unit-cell length c length_c	96.510 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	1.950 Å
Low-resolution limit resolution_low	48.260 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2460

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein

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

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

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

2eju__assembly_1__model_1

2eju__assembly_1__model_1 | I(q)

2eju__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein

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

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

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

2eju__assembly_1__model_1

2eju__assembly_1__model_1 | I(q)

2eju__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)