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9sdw

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

Method: X-RAY DIFFRACTION D_max: 81.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sdw
deposition_date	2025-08-14
title	tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus in complex with SAM-competitive compound
keywords	TrmD, Inhibitor, m7G, S. aureus, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	25.49 Å
rg_electron	25.12 Å
i0	23068500.00
molecular_weight	24487.0 kDa
excluded_volume	23602 Å³
envelope_volume	45867 Å³
shell_volume	16749 Å³
envelope_diameter	82.8 Å
shell_rg	30.04 Å
envelope_rg	25.02 Å
shape_rg	25.16 Å
total_rg	25.57 Å
total_atoms	1853
n_residues	230
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	81.5 Å
rg_real	25.70 Å
rg_real_error	0.68 Å
i0_real	2.3070e+07
i0_real_error	3.5340e+05
rg_reciprocal	25.64 Å
i0_reciprocal	23070000.0000
total_estimate	0.8270
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	21.0 Å
skewness	0.408
kurtosis	-0.734
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	2215000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.625; Smooth: 0.871

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	tRNA (guanine-N(1)-)-methyltransferase
formula_weight	30059.0 kDa
ec_number	2.1.1.228
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1883

HHHHHHSSGLVPRGSHMASKIDYLTLFPEMFDGVLNHSIMKRAQENNKLQINTVNFRDYAINKHNQVDDYPYGGGQGMVLKPEPVFNAMEDLDVTEQTRVILMCPQGEPFSHQKAVELSKADHIVFICGHYEGYDERIRTHLVTDEISMGDYVLTGGELPAMTMTDAIVRLIPGVLGNEQSHQDDSFSDGLLEFPQYTRPREFKGLTVPDVLLSGNHANIDAWRHEQKLIRTYNKRPDLIEKYPLTNADKQILERYKIGLKKG

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 2 non-polymer

description	1-[2-[4-(4-oxidanylidene-3,7-dihydropyrrolo[2,3-d]pyrimidin-5-yl)-1,2,3-triazol-1-yl]ethyl]guanidine
formula_weight	287.3 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	30

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6. Citations (1)

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length_a	126.875 Å
length_b	126.875 Å
length_c	126.875 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 43 3 2
int_tables_number	212
crystal_system	cubic

resolution	2.600 Å
resolution_low	44.860 Å
r_factor	0.2303
r_work	0.2275
r_free	0.2913

fit	/app/data/saxs_computation/sd/9sdw/9sdw.fit
pddf	/app/data/pr_computation/sd/9sdw/9sdw.pr.out
profile	/app/data/saxs_computation/sd/9sdw/9sdw.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction