SAXSdb — 5c1i

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

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

Thermus thermophilus HB27

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 3 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 A； PDBConstruct 1–251； UniProt 5–255 Author chain B； PDBConstruct 1–251； UniProt 5–255 Author chain C； PDBConstruct 1–251； UniProt 5–255 Author chain D； PDBConstruct 1–251； UniProt 5–255

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	5c1i
Deposition date deposition_date	2015-06-14
Structure title title	m1A58 tRNA methyltransferase mutant - D170A
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.

5c1i__assembly_1__model_1

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

Download this curve (.dat)

5c1i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5c1i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.70 Å
Rg (electron density)	29.54 Å
Total Rg	30.36 Å
Atom count	6965
Residues	878
Excluded volume	124660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5c1i__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 (3)

Entity 1 Entity 1 polymer

Description description	tRNA (adenine(58)-N(1))-methyltransferase TrmI
Molecular weight formula_weight	28097.5 kDa
EC 编号 ec_number	2.1.1.220
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6987

GPLLLKDRKGRAYLVFPKEGGVFHHHKGSVPHEALLEAGPGGVVRTHLGEELSVHRPTLEEYLLHMKRSATPTYPKDASAMVTLLDLAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEARPHHLAQAERNVRAFWQVENVRFHLGKLEEAELEEAAYDGVALALMEPWKVLEKAALALKPDRFLVAYLPNITQVLELVRAAEAHPFRLERVLEVGWREWEVRLPVAHPRFQQVGHTAFLVALRRWKGS

Source Source

Source organism organism	Thermus thermophilus HB27
NCBI taxonomy ID ncbi_taxonomy_id	262724
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5c1ia_
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	d5c1ib_
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	d5c1ic_
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	5c1iA00
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	5c1iB00
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	5c1iC00
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	5c1iD00
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	110.429 Å
Unit-cell length b length_b	110.429 Å
Unit-cell length c length_c	306.441 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	51.940 Å
R factor r_factor	—
R_work r_work	0.2002
R_free r_free	0.2686

m1A58 tRNA methyltransferase mutant - D170A

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

5c1i__assembly_1__model_1

5c1i__assembly_1__model_1 | I(q)

5c1i__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 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 - D170A

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

5c1i__assembly_1__model_1

5c1i__assembly_1__model_1 | I(q)

5c1i__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)