SAXSdb — 9sdw

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

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

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1-[2-[4-(4-oxidanylidene-3,7-dihydropyrrolo[2,3-d]pyrimidin-5-yl)-1,2,3-triazol-1-yl]ethyl]guanidine × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRMD_STAAS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–263； UniProt 2–245

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	9sdw
Deposition date deposition_date	2025-08-14
Structure title title	tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus in complex with SAM-competitive compound
Keywords keywords	TrmD, Inhibitor, m7G, S. aureus, TRANSFERASE; 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.

9sdw__assembly_1__model_1

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

Download this curve (.dat)

9sdw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9sdw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.59 Å
Rg (electron density)	25.13 Å
Total Rg	25.73 Å
Atom count	1853
Residues	230
Excluded volume	32782 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9sdw__assembly_1__model_1`	monomeric （1）	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	30059.0 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	1883

HHHHHHSSGLVPRGSHMASKIDYLTLFPEMFDGVLNHSIMKRAQENNKLQINTVNFRDYAINKHNQVDDYPYGGGQGMVLKPEPVFNAMEDLDVTEQTRVILMCPQGEPFSHQKAVELSKADHIVFICGHYEGYDERIRTHLVTDEISMGDYVLTGGELPAMTMTDAIVRLIPGVLGNEQSHQDDSFSDGLLEFPQYTRPREFKGLTVPDVLLSGNHANIDAWRHEQKLIRTYNKRPDLIEKYPLTNADKQILERYKIGLKKG

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-[2-[4-(4-oxidanylidene-3,7-dihydropyrrolo[2,3-d]pyrimidin-5-yl)-1,2,3-triazol-1-yl]ethyl]guanidine
Molecular weight formula_weight	287.3 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	30

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Unit-cell length a length_a	126.875 Å
Unit-cell length b length_b	126.875 Å
Unit-cell length c length_c	126.875 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	24

Space group space_group	P 43 3 2
Space-group number int_tables_number	212
Crystal system crystal_system	cubic

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	44.860 Å
R factor r_factor	0.2303
R_work r_work	0.2275
R_free r_free	0.2913

tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus in complex with SAM-competitive compound

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

9sdw__assembly_1__model_1

9sdw__assembly_1__model_1 | I(q)

9sdw__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

7. Citations (1)

tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus in complex with SAM-competitive compound

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

9sdw__assembly_1__model_1

9sdw__assembly_1__model_1 | I(q)

9sdw__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

7. Citations (1)