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9r32

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01887015

Method: X-RAY DIFFRACTION D_max: 144.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r32
deposition_date	2025-05-02
last_revision	2026-06-10
title	CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01887015
keywords	inhibitor, 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	43.46 Å
rg_electron	43.20 Å
i0	1546050000.00
molecular_weight	217670.0 kDa
excluded_volume	211250 Å³
envelope_volume	375400 Å³
shell_volume	71212 Å³
envelope_diameter	144.1 Å
shell_rg	48.98 Å
envelope_rg	43.01 Å
shape_rg	43.21 Å
total_rg	43.38 Å
total_atoms	16451
n_residues	2004
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	144.4 Å
rg_real	43.39 Å
rg_real_error	1.46 Å
i0_real	1.5460e+09
i0_real_error	2.9190e+07
rg_reciprocal	43.46 Å
i0_reciprocal	1546000000.0000
total_estimate	0.8228
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.1 Å
skewness	0.254
kurtosis	-0.498
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	115600000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Lysine--tRNA ligase
formula_weight	61459.1 kDa
ec_number	6.1.1.6
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	17853

MAHHHHHHMGTLEAQTQGPGSHYTDNRYKMMECIKDAGRPFYPHKFKISMSLPAYALKYGNVENGYIDKDTTLSLSGRVTSIRSSSSKLIFYDIFCEEQKVQIIANIMEHDISTGEFSVSHSEIRRGDVVGFTGFPGKSKRGELSLFSKSVVLLSPCYHMLPTAISGLKDQEVRYRQRYLDLMLNEESRKVFKLRSRAIKYIRNYFDRLGFLEVETPMLNMIYGGAAARPFITYHNELETQLYMRIAPELYLKQLIVGGLDKVYEIGKNFRNEGIDLTHNPEFTAMEFYMAYADYYDLMDLTEELISGLVLEIHGSLKIPYHPDGPEGKCIEIDFTTPWKRFSFVEEIESGLGEKLKRPLDSQENIDFMVEMCEKHEIELPHPRTAAKLLDKLAGHFVETKCTNPSFIIDHPQTMSPLAKWHREKPEMTERFELFVLGKELCNAYTELNEPLQQRKFFEQQADAKASGDVEACPIDETFCLALEHGLPPTGGWGLGIDRLIMFLADKNNIKEVILFPAMRNVKQNAQHSNQHSGN

Source

organism	Cryptosporidium parvum Iowa II
ncbi_taxonomy_id	353152
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-azanyl-6-[[(1~{S},3~{S})-1-oxidanyl-3-(trifluoromethyl)cyclohexyl]methyl]-4-(trifluoromethyl)-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one
formula_weight	398.3 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	nat
entity_count	4

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	9

Entity 6 non-polymer

description	LYSINE
formula_weight	147.2 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1376

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6. Citations (1)

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length_a	73.153 Å
length_b	119.425 Å
length_c	142.760 Å
angle_alpha	90.00 °
angle_beta	90.31 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.900 Å
resolution_low	91.768 Å
r_factor	—
r_work	0.1802
r_free	0.2064

fit	/app/data/saxs_computation/r3/9r32/9r32.fit
pddf	/app/data/pr_computation/r3/9r32/9r32.pr.out
profile	/app/data/saxs_computation/r3/9r32/9r32.dat