← Back to search

9qc4

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01869767

Method: X-RAY DIFFRACTION D_max: 95.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qc4
deposition_date	2025-03-04
title	CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01869767
keywords	ligase, inhibitor; LIGASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	29.21 Å
rg_electron	28.91 Å
i0	82312800.00
molecular_weight	47249.0 kDa
excluded_volume	45439 Å³
envelope_volume	85797 Å³
shell_volume	26444 Å³
envelope_diameter	97.8 Å
shell_rg	34.11 Å
envelope_rg	28.92 Å
shape_rg	28.89 Å
total_rg	29.35 Å
total_atoms	3588
n_residues	458
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

▼

3. P(r) Analysis (GNOM)

dmax	95.6 Å
rg_real	29.41 Å
rg_real_error	0.82 Å
i0_real	8.2310e+07
i0_real_error	1.2140e+06
rg_reciprocal	29.32 Å
i0_reciprocal	82310000.0000
total_estimate	0.8568
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	26.6 Å
skewness	0.463
kurtosis	-0.542
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	8202000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.833; Smooth: 0.833

▶

4. Crystallography & Experiment

▶

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	3619

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	6-azanyl-1-[2-(azetidin-3-yl)ethyl]-2-cycloheptyl-4-ethoxy-pyrazolo[3,4-d]pyrimidin-3-one
formula_weight	374.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	31

▶

6. Citations (1)

▶

length_a	83.983 Å
length_b	83.983 Å
length_c	147.324 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	2.601 Å
resolution_low	46.275 Å
r_factor	—
r_work	0.2318
r_free	0.2921

fit	/app/data/saxs_computation/qc/9qc4/9qc4.fit
pddf	/app/data/pr_computation/qc/9qc4/9qc4.pr.out
profile	/app/data/saxs_computation/qc/9qc4/9qc4.dat

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01869767

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