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9sdv

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

Method: X-RAY DIFFRACTION D_max: 81.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sdv
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	25.60 Å
rg_electron	25.08 Å
i0	12200900.00
molecular_weight	26203.0 kDa
excluded_volume	32756 Å³
envelope_volume	45445 Å³
shell_volume	16696 Å³
envelope_diameter	83.4 Å
shell_rg	29.86 Å
envelope_rg	24.87 Å
shape_rg	25.13 Å
total_rg	25.59 Å
total_atoms	1851
n_residues	231
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	81.9 Å
rg_real	25.82 Å
rg_real_error	0.64 Å
i0_real	1.2200e+07
i0_real_error	1.6930e+05
rg_reciprocal	25.76 Å
i0_reciprocal	12200000.0000
total_estimate	0.8275
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.1 Å
skewness	0.416
kurtosis	-0.714
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	1789000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.654; Smooth: 0.842

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	1915

HHHHHHSSGLVPRGSHMASKIDYLTLFPEMFDGVLNHSIMKRAQENNKLQINTVNFRDYAINKHNQVDDYPYGGGQGMVLKPEPVFNAMEDLDVTEQTRVILMCPQGEPFSHQKAVELSKADHIVFICGHYEGYDERIRTHLVTDEISMGDYVLTGGELPAMTMTDAIVRLIPGVLGNEQSHQDDSFSDGLLEFPQYTRPREFKGLTVPDVLLSGNHANIDAWRHEQKLIRTYNKRPDLIEKYPLTNADKQILERYKIGLKKG

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	N-[4-(aminomethyl)benzyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide
formula_weight	314.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	58

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6. Citations (1)

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length_a	126.695 Å
length_b	126.695 Å
length_c	126.695 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	2.500 Å
resolution_low	42.230 Å
r_factor	0.2252
r_work	0.2224
r_free	0.2804

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