SAXSdb — 5c0o

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

tRNA (adenine(58)-N(1))-methyltransferase TrmI

Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	S-ADENOSYLMETHIONINE × 4 SULFATE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRMI_THET2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–255； UniProt 1–255 Author chain F； PDBConstruct 1–255； UniProt 1–255 Author chain G； PDBConstruct 1–255； UniProt 1–255 Author chain H； PDBConstruct 1–255； UniProt 1–255

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	5c0o
Deposition date deposition_date	2015-06-12
Structure title title	m1A58 tRNA methyltransferase mutant - Y78A
Keywords keywords	transferase, TrmI, m1A; 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.

5c0o__assembly_1__model_1

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

Download this curve (.dat)

5c0o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5c0o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.16 Å
Rg (electron density)	30.07 Å
Total Rg	30.86 Å
Atom count	7132
Residues	918
Excluded volume	127470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5c0o__assembly_1__model_1`	tetrameric （4）	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	tRNA (adenine(58)-N(1))-methyltransferase TrmI
Molecular weight formula_weight	28549.0 kDa
EC 编号 ec_number	2.1.1.220
Mutation mutation	Y78A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H
Atom count atom_count	7264

MAWPGPLLLKDRKGRAYLVFPKEGGVFHHHKGSVPHEALLEAGPGGVVRTHLGEELSVHRPTLEEYLLHMKRSATPTAPKDASAMVTLLDLAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEARPHHLAQAERNVRAFWQVENVRFHLGKLEEAELEEAAYDGVALDLMEPWKVLEKAALALKPDRFLVAYLPNITQVLELVRAAEAHPFRLERVLEVGWREWEVRLPVAHPRFQQVGHTAFLVALRRWKAS

Source Source

Source organism organism	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
NCBI taxonomy ID ncbi_taxonomy_id	262724
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	4

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	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	132

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5c0oe_
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.66.1.0 — automated matches

Domain ID domain_id	d5c0of_
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.66.1.0 — automated matches

Domain ID domain_id	d5c0og_
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.66.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5c0oE02
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	5c0oF02
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	5c0oG02
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	5c0oH00
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

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Unit-cell length a length_a	76.540 Å
Unit-cell length b length_b	79.860 Å
Unit-cell length c length_c	184.000 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	16

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

Resolution resolution	2.620 Å
Low-resolution limit resolution_low	52.923 Å
R factor r_factor	—
R_work r_work	0.2352
R_free r_free	0.2824

m1A58 tRNA methyltransferase mutant - Y78A

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

tRNA (adenine(58)-N(1))-methyltransferase TrmI

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

5c0o__assembly_1__model_1

5c0o__assembly_1__model_1 | I(q)

5c0o__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) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

m1A58 tRNA methyltransferase mutant - Y78A

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

tRNA (adenine(58)-N(1))-methyltransferase TrmI

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

5c0o__assembly_1__model_1

5c0o__assembly_1__model_1 | I(q)

5c0o__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) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)