SAXSdb — 1oy5

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

tRNA (Guanine-N(1)-)-methyltransferase

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	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRMD_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–257； UniProt 1–257 Author chain B； PDBConstruct 1–257； UniProt 1–257 Author chain C； PDBConstruct 1–257； UniProt 1–257

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	1oy5
Deposition date deposition_date	2003-04-03
Structure title title	Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus
Keywords keywords	;structural genomics, trmD, tRNA (m1G37) methyltransferase, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, 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.

1oy5__assembly_1__model_1

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

Download this curve (.dat)

1oy5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1oy5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.89 Å
Rg (electron density)	23.73 Å
Total Rg	24.55 Å
Atom count	3536
Residues	436
Excluded volume	64235 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1oy5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1oy5__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 (2)

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1oy5a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.4 — tRNA(m1G37)-methyltransferase TrmD

Domain ID domain_id	d1oy5b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.4 — tRNA(m1G37)-methyltransferase TrmD

Domain ID domain_id	d1oy5c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.4 — tRNA(m1G37)-methyltransferase TrmD

CATH v4.4 (6 domains)

Domain ID domain_id	1oy5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1oy5A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1270 — Trp Operon Repressor; Chain A
Homologous superfamily homologous superfamily	20 — tRNA(m1g37)methyltransferase, domain 2

Domain ID domain_id	1oy5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1oy5B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1270 — Trp Operon Repressor; Chain A
Homologous superfamily homologous superfamily	20 — tRNA(m1g37)methyltransferase, domain 2

Domain ID domain_id	1oy5C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1oy5C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1270 — Trp Operon Repressor; Chain A
Homologous superfamily homologous superfamily	20 — tRNA(m1g37)methyltransferase, domain 2

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Unit-cell length a length_a	153.351 Å
Unit-cell length b length_b	96.139 Å
Unit-cell length c length_c	57.426 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2805
R_work r_work	0.2794
R_free r_free	0.3003

Description description	tRNA (Guanine-N(1)-)-methyltransferase
Molecular weight formula_weight	29693.6 kDa
EC 编号 ec_number	2.1.1.31
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5379

Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus

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

tRNA (Guanine-N(1)-)-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

1oy5__assembly_1__model_1

1oy5__assembly_1__model_1 | I(q)

1oy5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus

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

tRNA (Guanine-N(1)-)-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

1oy5__assembly_1__model_1

1oy5__assembly_1__model_1 | I(q)

1oy5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)