← Back to search

9r3r

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01827593

Method: X-RAY DIFFRACTION D_max: 106.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9r3r
deposition_date	2025-05-06
title	CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01827593
keywords	inhibitor, LIGASE; LIGASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.50 Å
rg_electron	31.91 Å
i0	393611000.00
molecular_weight	107580.0 kDa
excluded_volume	104520 Å³
envelope_volume	176670 Å³
shell_volume	45837 Å³
envelope_diameter	116.2 Å
shell_rg	39.00 Å
envelope_rg	32.15 Å
shape_rg	31.87 Å
total_rg	32.37 Å
total_atoms	8134
n_residues	996
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	106.4 Å
rg_real	32.48 Å
rg_real_error	0.78 Å
i0_real	3.9360e+08
i0_real_error	6.1080e+06
rg_reciprocal	32.49 Å
i0_reciprocal	393600000.0000
total_estimate	0.8897
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.9 Å
skewness	0.344
kurtosis	-0.361
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	61120000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.912

▶

4. Crystallography & Experiment

▶

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	9097

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	6-azanyl-2-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-4-(trifluoromethyl)-1~{H}-pyrrolo[3,4-c]pyridin-3-one
formula_weight	365.3 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	940

▶

6. Citations (1)

▶

length_a	72.759 Å
length_b	116.265 Å
length_c	142.086 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	1.500 Å
resolution_low	46.618 Å
r_factor	—
r_work	0.1576
r_free	0.1806

fit	/app/data/saxs_computation/r3/9r3r/9r3r.fit
pddf	/app/data/pr_computation/r3/9r3r/9r3r.pr.out
profile	/app/data/saxs_computation/r3/9r3r/9r3r.dat