SAXSdb — 3bt7

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

tRNA (uracil-5-)-methyltransferase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	;RNA (5'-D(PGPCPUPGPUPGP(5MU)PUPCPGPAPUPCPCPAPCPAPGP*C)-3') ; × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	;RNA (5'-D(PGPCPUPGPUPGP(5MU)PUPCPGPAPUPCPCPAPCPAPGP*C)-3') ; × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRMA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–369； UniProt 1–366 Author chain B； PDBConstruct 4–369； UniProt 1–366

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	3bt7
Deposition date deposition_date	2007-12-27
Structure title title	Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue
Keywords keywords	methyluridine, methyltransferase, TrmA, RUMT, S-adenosyl-L-methionine, tRNA processing, TRANSFERASE-RNA COMPLEX; TRANSFERASE/RNA
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.

3bt7__assembly_1__model_1

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

Download this curve (.dat)

3bt7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bt7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.69 Å
Rg (electron density)	21.93 Å
Total Rg	22.67 Å
Atom count	3357
Residues	387
Excluded volume	58104 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bt7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bt7__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 (3)

Entity 1 Entity 1 polymer

Description description	tRNA (uracil-5-)-methyltransferase
Molecular weight formula_weight	42298.1 kDa
EC 编号 ec_number	2.1.1.35
Mutation mutation	E358Q
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6982

GSHMTPEHLPTEQYEAQLAEKVVRLQSMMAPFSDLVPEVFRSPVSHYRMRAEFRIWHDGDDLYHIIFDQQTKSRIRVDSFPAASELINQLMTAMIAGVRNNPVLRHKLFQIDYLTTLSNQAVVSLLYHKKLDDEWRQEAEALRDALRAQNLNVHLIGRATKTKIELDQDYIDERLPVAGKEMIYRQVENSFTQPNAAMNIQMLEWALDVTKGSKGDLLELYCGNGNFSLALARNFDRVLATEIAKPSVAAAQYNIAANHIDNVQIIRMAAEEFTQAMNGVREFNRLQGIDLKSYQCETIFVDPPRSGLDSETEKMVQAYPRILYISCNPETLCKNLETLSQTHKVERLALFDQFPYTHHMQCGVLLTAK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;RNA (5'-D(PGPCPUPGPUPGP(5MU)PUPCPGPAPUPCPCPAPCPAPGP*C)-3') ;
Molecular weight formula_weight	6044.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D

GCUGUGUUCGAUCCACAGC

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	261

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3bt7A01
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	3bt7A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	1070 —

Domain ID domain_id	3bt7B01
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	3bt7B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	1070 —

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Unit-cell length a length_a	184.407 Å
Unit-cell length b length_b	70.131 Å
Unit-cell length c length_c	107.950 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	120.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.430 Å
Low-resolution limit resolution_low	35.070 Å
R factor r_factor	0.2297
R_work r_work	0.2251
R_free r_free	0.2863

Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue

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

tRNA (uracil-5-)-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

3bt7__assembly_1__model_1

3bt7__assembly_1__model_1 | I(q)

3bt7__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue

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

tRNA (uracil-5-)-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

3bt7__assembly_1__model_1

3bt7__assembly_1__model_1 | I(q)

3bt7__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 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)