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9qc3

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01993593

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	9qc3
deposition_date	2025-03-04
title	CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01993593
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	29.24 Å
rg_electron	28.97 Å
i0	84023700.00
molecular_weight	47720.0 kDa
excluded_volume	45875 Å³
envelope_volume	84368 Å³
shell_volume	26090 Å³
envelope_diameter	97.2 Å
shell_rg	33.98 Å
envelope_rg	28.77 Å
shape_rg	28.95 Å
total_rg	29.39 Å
total_atoms	3622
n_residues	462
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	29.45 Å
rg_real_error	0.79 Å
i0_real	8.4020e+07
i0_real_error	1.3480e+06
rg_reciprocal	29.36 Å
i0_reciprocal	84020000.0000
total_estimate	0.8545
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	26.9 Å
skewness	0.454
kurtosis	-0.569
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	7980000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.802; Smooth: 0.885

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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	3704

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-4-methoxy-6-[(1~{R},2~{S})-2-oxidanylcycloheptyl]-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one
formula_weight	292.3 kDa
src_method	nat
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	82

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6. Citations (1)

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length_a	83.669 Å
length_b	83.669 Å
length_c	147.261 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	2.280 Å
resolution_low	72.853 Å
r_factor	—
r_work	0.2140
r_free	0.2769

fit	/app/data/saxs_computation/qc/9qc3/9qc3.fit
pddf	/app/data/pr_computation/qc/9qc3/9qc3.pr.out
profile	/app/data/saxs_computation/qc/9qc3/9qc3.dat

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01993593

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