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9r3f

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01932549

Method: X-RAY DIFFRACTION D_max: 109.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r3f
deposition_date	2025-05-05
last_revision	2026-06-10
title	CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01932549
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	32.56 Å
rg_electron	31.98 Å
i0	393457000.00
molecular_weight	107610.0 kDa
excluded_volume	104530 Å³
envelope_volume	177990 Å³
shell_volume	46027 Å³
envelope_diameter	116.9 Å
shell_rg	39.16 Å
envelope_rg	32.31 Å
shape_rg	31.94 Å
total_rg	32.43 Å
total_atoms	8136
n_residues	995
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	109.1 Å
rg_real	32.55 Å
rg_real_error	0.83 Å
i0_real	3.9350e+08
i0_real_error	6.0160e+06
rg_reciprocal	32.56 Å
i0_reciprocal	393500000.0000
total_estimate	0.8845
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.9 Å
skewness	0.346
kurtosis	-0.360
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	64750000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.950

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Lysine--tRNA ligase
formula_weight	61459.1 kDa
ec_number	6.1.1.6
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8936

MAHHHHHHMGTLEAQTQGPGSHYTDNRYKMMECIKDAGRPFYPHKFKISMSLPAYALKYGNVENGYIDKDTTLSLSGRVTSIRSSSSKLIFYDIFCEEQKVQIIANIMEHDISTGEFSVSHSEIRRGDVVGFTGFPGKSKRGELSLFSKSVVLLSPCYHMLPTAISGLKDQEVRYRQRYLDLMLNEESRKVFKLRSRAIKYIRNYFDRLGFLEVETPMLNMIYGGAAARPFITYHNELETQLYMRIAPELYLKQLIVGGLDKVYEIGKNFRNEGIDLTHNPEFTAMEFYMAYADYYDLMDLTEELISGLVLEIHGSLKIPYHPDGPEGKCIEIDFTTPWKRFSFVEEIESGLGEKLKRPLDSQENIDFMVEMCEKHEIELPHPRTAAKLLDKLAGHFVETKCTNPSFIIDHPQTMSPLAKWHREKPEMTERFELFVLGKELCNAYTELNEPLQQRKFFEQQADAKASGDVEACPIDETFCLALEHGLPPTGGWGLGIDRLIMFLADKNNIKEVILFPAMRNVKQNAQHSNQHSGN

Source

organism	Cryptosporidium parvum Iowa II
ncbi_taxonomy_id	353152
host_organism	Escherichia coli

Entity 2 non-polymer

description	LYSINE
formula_weight	147.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	;2-azanyl-6-[[(1~{R},3~{S})-1-(2-azanylethyl)-3-(trifluoromethyl)cyclohexyl]methyl]-4-(trifluoromethyl)-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one ;
formula_weight	425.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	nat
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	796

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6. Citations (1)

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length_a	73.152 Å
length_b	116.852 Å
length_c	143.262 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 21 21
int_tables_number	18
crystal_system	—

resolution	2.300 Å
resolution_low	46.924 Å
r_factor	—
r_work	0.2137
r_free	0.2612

fit	/app/data/saxs_computation/r3/9r3f/9r3f.fit
pddf	/app/data/pr_computation/r3/9r3f/9r3f.pr.out
profile	/app/data/saxs_computation/r3/9r3f/9r3f.dat