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9v9m

Methionyl-tRNA synthetase from Staphylococcus aureus in complex with an inhibitor

Method: X-RAY DIFFRACTION D_max: 96.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v9m
deposition_date	2025-06-01
last_revision	2026-06-03
title	Methionyl-tRNA synthetase from Staphylococcus aureus in complex with an inhibitor
keywords	methionyl-tRNA synthetase, complex, LIGASE; LIGASE
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	27.18 Å
rg_electron	26.83 Å
i0	97108100.00
molecular_weight	53728.0 kDa
excluded_volume	52907 Å³
envelope_volume	85875 Å³
shell_volume	28082 Å³
envelope_diameter	101.5 Å
shell_rg	32.56 Å
envelope_rg	27.18 Å
shape_rg	26.78 Å
total_rg	27.34 Å
total_atoms	4088
n_residues	507
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	96.6 Å
rg_real	27.41 Å
rg_real_error	1.00 Å
i0_real	9.7110e+07
i0_real_error	1.5960e+06
rg_reciprocal	27.34 Å
i0_reciprocal	97100000.0000
total_estimate	0.8285
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.6 Å
skewness	0.582
kurtosis	-0.140
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	16240000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.653; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.967

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Methionine--tRNA ligase
formula_weight	61104.0 kDa
ec_number	6.1.1.10
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AAA
atom_count	4310

MGSSHHHHHHSAKETFYITTPIYYPSGNLHIGHAYSTVAGDVIARYKRMQGYDVRYLTGTDEHGQKIQEKAQKAGKTEIEYLDEMIAGIKQLWAKLEISNDDFIRTTEERHKHVVEQVFERLLKQGDIYLGEYEGWYSVPDETYYTESQLVDPQYENGKIIGGKSPDSGHEVELVKEESYFFNISKYTDRLLEFYDQNPDFIQPPSRKNEMINNFIKPGLADLAVSRTSFNWGVHVPSNPKHVVYVWIDALVNYISALGYLSDDESLFNKYWPADIHLMAKEIVRFHSIIWPILLMALDLPLPKKVFAHGWILMKDGKMSKSKGNVVDPNILIDRYGLDATRYYLMRELPFGSDGVFTPEAFVERTNFDLANDLGNLVNRTISMVNKYFDGELPAYQGPLHELDEEMEAMALETVKSYTESMESLQFSVALSTVWKFISRTNKYIDETTPWVLAKDDSQKDMLGNVMAHLVENIRYAAVLLRPFLTHAPKEIFEQLNINNPQFMEFSSLEQYGVLNESIMVTGQPKPIFP

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 2 non-polymer

description	AZD8186
formula_weight	457.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	8

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	213

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6. Citations (1)

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length_a	59.627 Å
length_b	77.171 Å
length_c	119.464 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.501 Å
resolution_low	23.631 Å
r_factor	—
r_work	0.2231
r_free	0.2560

fit	/app/data/saxs_computation/v9/9v9m/9v9m.fit
pddf	/app/data/pr_computation/v9/9v9m/9v9m.pr.out
profile	/app/data/saxs_computation/v9/9v9m/9v9m.dat

Methionyl-tRNA synthetase from Staphylococcus aureus in complex with an inhibitor

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