SAXSdb — 4yqn

▼

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

tRNA (guanine-N(1)-)-methyltransferase

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	6-{[(1R,3S,4R)-3-hydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyridine-3-carboxamide × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRMD_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–254； UniProt 1–246

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4yqn
Deposition date deposition_date	2015-03-13
Structure title title	Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Keywords keywords	TrmD, SAM-binding, knot, transferase-transferase inhibitor complex; transferase/transferase inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4yqn__assembly_1__model_1

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

Download this curve (.dat)

4yqn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4yqn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.30 Å
Rg (electron density)	24.08 Å
Total Rg	24.93 Å
Atom count	3770
Residues	474
Excluded volume	67313 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4yqn__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	tRNA (guanine-N(1)-)-methyltransferase
Molecular weight formula_weight	28384.6 kDa
EC 编号 ec_number	2.1.1.228
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	2026

GLVPRGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS

Source Source

Source organism organism	Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
NCBI taxonomy ID ncbi_taxonomy_id	71421
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	6-{[(1R,3S,4R)-3-hydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyridine-3-carboxamide
Molecular weight formula_weight	251.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	136

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4yqna1
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	d4yqna2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	4yqnA01
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	4yqnA02
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

▶

Unit-cell length a length_a	94.684 Å
Unit-cell length b length_b	94.684 Å
Unit-cell length c length_c	177.761 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	39.951 Å
R factor r_factor	0.1803
R_work r_work	0.1752
R_free r_free	0.2267

Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds

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

4yqn__assembly_1__model_1

4yqn__assembly_1__model_1 | I(q)

4yqn__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds

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

4yqn__assembly_1__model_1

4yqn__assembly_1__model_1 | I(q)

4yqn__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)