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9v9d

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

Method: X-RAY DIFFRACTION D_max: 96.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v9d
deposition_date	2025-05-30
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	27.02 Å
rg_electron	26.61 Å
i0	98346100.00
molecular_weight	53771.0 kDa
excluded_volume	52795 Å³
envelope_volume	84931 Å³
shell_volume	27939 Å³
envelope_diameter	99.2 Å
shell_rg	32.43 Å
envelope_rg	26.95 Å
shape_rg	26.56 Å
total_rg	27.14 Å
total_atoms	4087
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	96.0 Å
rg_real	27.24 Å
rg_real_error	0.85 Å
i0_real	9.8350e+07
i0_real_error	1.4000e+06
rg_reciprocal	27.17 Å
i0_reciprocal	98340000.0000
total_estimate	0.8183
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.7 Å
skewness	0.577
kurtosis	-0.143
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	17460000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.653; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.720; Smooth: 0.955

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	4254

MGSSHHHHHHSAKETFYITTPIYYPSGNLHIGHAYSTVAGDVIARYKRMQGYDVRYLTGTDEHGQKIQEKAQKAGKTEIEYLDEMIAGIKQLWAKLEISNDDFIRTTEERHKHVVEQVFERLLKQGDIYLGEYEGWYSVPDETYYTESQLVDPQYENGKIIGGKSPDSGHEVELVKEESYFFNISKYTDRLLEFYDQNPDFIQPPSRKNEMINNFIKPGLADLAVSRTSFNWGVHVPSNPKHVVYVWIDALVNYISALGYLSDDESLFNKYWPADIHLMAKEIVRFHSIIWPILLMALDLPLPKKVFAHGWILMKDGKMSKSKGNVVDPNILIDRYGLDATRYYLMRELPFGSDGVFTPEAFVERTNFDLANDLGNLVNRTISMVNKYFDGELPAYQGPLHELDEEMEAMALETVKSYTESMESLQFSVALSTVWKFISRTNKYIDETTPWVLAKDDSQKDMLGNVMAHLVENIRYAAVLLRPFLTHAPKEIFEQLNINNPQFMEFSSLEQYGVLNESIMVTGQPKPIFP

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 2 non-polymer

description	;9-[(1R)-1-[[3,5-bis(chloranyl)phenyl]amino]ethyl]-N,N-dimethyl-2-morpholin-4-yl-4-oxidanylidene-pyrido[1,2-a]pyrimidine-7-carboxamide ;
formula_weight	490.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	167

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6. Citations (1)

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length_a	53.961 Å
length_b	74.132 Å
length_c	116.719 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	26.981 Å
r_factor	—
r_work	0.2297
r_free	0.2570

fit	/app/data/saxs_computation/v9/9v9d/9v9d.fit
pddf	/app/data/pr_computation/v9/9v9d/9v9d.pr.out
profile	/app/data/saxs_computation/v9/9v9d/9v9d.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