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9r3g

;CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum / Plasmodium falciparum chimera COMPLEXED WITH L-LYSINE AND INHIBITOR DDD02174286 ;

Method: X-RAY DIFFRACTION D_max: 109.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r3g
deposition_date	2025-05-05
last_revision	2026-06-10
title	;CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum / Plasmodium falciparum chimera COMPLEXED WITH L-LYSINE AND INHIBITOR DDD02174286 ;
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	32.52 Å
rg_electron	31.91 Å
i0	398990000.00
molecular_weight	108430.0 kDa
excluded_volume	105340 Å³
envelope_volume	178350 Å³
shell_volume	46140 Å³
envelope_diameter	117.0 Å
shell_rg	39.21 Å
envelope_rg	32.21 Å
shape_rg	31.87 Å
total_rg	32.38 Å
total_atoms	8196
n_residues	998
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	109.7 Å
rg_real	32.49 Å
rg_real_error	0.86 Å
i0_real	3.9900e+08
i0_real_error	5.7360e+06
rg_reciprocal	32.50 Å
i0_reciprocal	399000000.0000
total_estimate	0.8835
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.1 Å
skewness	0.339
kurtosis	-0.371
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	67850000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Lysine-tRNA ligase
formula_weight	61464.1 kDa
ec_number	6.1.1.6
mutation	P272T, N293V, A309S
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9068

MAHHHHHHMGTLEAQTQGPGSHYTDNRYKMMECIKDAGRPFYPHKFKISMSLPAYALKYGNVENGYIDKDTTLSLSGRVTSIRSSSSKLIFYDIFCEEQKVQIIANIMEHDISTGEFSVSHSEIRRGDVVGFTGFPGKSKRGELSLFSKSVVLLSPCYHMLPTAISGLKDQEVRYRQRYLDLMLNEESRKVFKLRSRAIKYIRNYFDRLGFLEVETPMLNMIYGGAAARPFITYHNELETQLYMRIATELYLKQLIVGGLDKVYEIGKVFRNEGIDLTHNPEFTSMEFYMAYADYYDLMDLTEELISGLVLEIHGSLKIPYHPDGPEGKCIEIDFTTPWKRFSFVEEIESGLGEKLKRPLDSQENIDFMVEMCEKHEIELPHPRTAAKLLDKLAGHFVETKCTNPSFIIDHPQTMSPLAKWHREKPEMTERFELFVLGKELCNAYTELNEPLQQRKFFEQQADAKASGDVEACPIDETFCLALEHGLPPTGGWGLGIDRLIMFLADKNNIKEVILFPAMRNVKQNAQHSNQHSGN

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-(1,7-diazaspiro[3.5]nonan-7-yl)ethyl]-3-(trifluoromethyl)cyclohexyl]methyl]-4-(trifluoromethyl)-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one ;
formula_weight	534.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	nat
entity_count	1

Entity 6 non-polymer

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

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	854

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6. Citations (1)

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length_a	72.808 Å
length_b	116.579 Å
length_c	142.991 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	1.900 Å
resolution_low	61.830 Å
r_factor	—
r_work	0.1600
r_free	0.1897

fit	/app/data/saxs_computation/r3/9r3g/9r3g.fit
pddf	/app/data/pr_computation/r3/9r3g/9r3g.pr.out
profile	/app/data/saxs_computation/r3/9r3g/9r3g.dat