SAXSdb — 4yvi

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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–RNA	Homooligomer	Protein 2 RNA 1	tRNA × 1 SINEFUNGIN × 2	Consistent with all polymers

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 21–266； UniProt 1–246 Author chain B； PDBConstruct 21–266； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4yvi
Deposition date deposition_date	2015-03-20
Structure title title	Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA
Keywords keywords	MTase, SPOUT, tRNA, 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.

4yvi__assembly_1__model_1

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

Download this curve (.dat)

4yvi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4yvi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.08 Å
Rg (electron density)	32.78 Å
Total Rg	33.31 Å
Atom count	5421
Residues	559
Excluded volume	90933 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4yvi__assembly_1__model_1`	trimeric （3）	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 (guanine-N(1)-)-methyltransferase
Molecular weight formula_weight	29750.0 kDa
EC 编号 ec_number	2.1.1.228
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	5421

MGSSHHHHHHSSGLVPRGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS

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 polymer

Description description	tRNA
Molecular weight formula_weight	23858.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

UGGGAGGUCGUCUAACGGUAGGACGGCGGACUCUGGAUCCGCUGGUGGAGGUUCGAGUCCUCCCCUCCCAGCCA

Entity 3 Entity 3 non-polymer

Description description	SINEFUNGIN
Molecular weight formula_weight	381.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4yviA01
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	4yviA02
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	4yviB01
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	4yviB02
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	86.770 Å
Unit-cell length b length_b	86.770 Å
Unit-cell length c length_c	227.010 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.010 Å
Low-resolution limit resolution_low	34.529 Å
R factor r_factor	0.2215
R_work r_work	0.2183
R_free r_free	0.2830

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA

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

4yvi__assembly_1__model_1

4yvi__assembly_1__model_1 | I(q)

4yvi__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 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA

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

4yvi__assembly_1__model_1

4yvi__assembly_1__model_1 | I(q)

4yvi__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 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)