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9qdj

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD018870911

Method: X-RAY DIFFRACTION D_max: 96.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdj
deposition_date	2025-03-06
title	CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD018870911
keywords	ligase, inhibitor; 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	29.31 Å
rg_electron	29.00 Å
i0	86035100.00
molecular_weight	48206.0 kDa
excluded_volume	46307 Å³
envelope_volume	86863 Å³
shell_volume	26622 Å³
envelope_diameter	96.8 Å
shell_rg	34.20 Å
envelope_rg	28.93 Å
shape_rg	28.98 Å
total_rg	29.43 Å
total_atoms	3658
n_residues	468
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	96.8 Å
rg_real	29.50 Å
rg_real_error	0.86 Å
i0_real	8.6040e+07
i0_real_error	1.3700e+06
rg_reciprocal	29.42 Å
i0_reciprocal	86030000.0000
total_estimate	0.8593
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	26.9 Å
skewness	0.451
kurtosis	-0.553
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	8234000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.882

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Lysine--tRNA ligase 1
formula_weight	58189.7 kDa
ec_number	6.1.1.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3670

MGSSHHHHHHSSGENLYFQGHMSAADTAEDLPEQFRIRRDKRARLLAQGRDPYPVAVPRTHTLAEVRAAHPDLPIDTATEDIVGVAGRVIFARNSGKLCFATLQDGDGTQLQVMISLDKVGQAALDAWKADVDLGDIVYVHGAVISSRRGELSVLADCWRIAAKSLRPLPVAHKEMSEESRVRQRYVDLIVRPEARAVARLRIAVVRAIRTALQRRGFLEVETPVLQTLAGGAAARPFATHSNALDIDLYLRIAPELFLKRCIVGGFDKVFELNRVFRNEGADSTHSPEFSMLETYQTYGTYDDSAVVTRELIQEVADEAIGTRQLPLPDGSVYDIDGEWATIQMYPSLSVALGEEITPQTTVDRLRGIADSLGLEKDPAIHDNRGFGHGKLIEELWERTVGKSLSAPTFVKDFPVQTTPLTRQHRSIPGVTEKWDLYLRGIELATGYSELSDPVVQRERFADQARAAAAGDDEAMVLDEDFLAALEYGMPPCTGTGMGIDRLLMSLTGLSIRETVLFPIVRPHSN

Source

organism	Mycobacterium tuberculosis
ncbi_taxonomy_id	1773
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	LYSINE
formula_weight	147.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-azanyl-6-[(1~{S})-2,2-bis(fluoranyl)cyclohexyl]-4-methoxy-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one
formula_weight	298.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	12

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6. Citations (1)

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length_a	83.701 Å
length_b	83.701 Å
length_c	147.691 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	2.597 Å
resolution_low	46.225 Å
r_factor	—
r_work	0.2601
r_free	0.3181

fit	/app/data/saxs_computation/qd/9qdj/9qdj.fit
pddf	/app/data/pr_computation/qd/9qdj/9qdj.pr.out
profile	/app/data/saxs_computation/qd/9qdj/9qdj.dat

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD018870911

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