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9yon

;Crystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with inhibitor YNW69 ;

Method: X-RAY DIFFRACTION D_max: 88.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yon
deposition_date	2025-10-13
last_revision	2025-10-22
title	;Crystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with inhibitor YNW69 ;
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, 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	26.35 Å
rg_electron	25.73 Å
i0	100867000.00
molecular_weight	53165.0 kDa
excluded_volume	51546 Å³
envelope_volume	85214 Å³
shell_volume	28467 Å³
envelope_diameter	93.5 Å
shell_rg	32.24 Å
envelope_rg	26.13 Å
shape_rg	25.69 Å
total_rg	26.30 Å
total_atoms	4009
n_residues	493
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	88.6 Å
rg_real	26.39 Å
rg_real_error	0.83 Å
i0_real	1.0090e+08
i0_real_error	1.4910e+06
rg_reciprocal	26.38 Å
i0_reciprocal	100900000.0000
total_estimate	0.8773
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.1 Å
skewness	0.392
kurtosis	-0.325
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	20830000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.925

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Proline--tRNA ligase
formula_weight	58986.5 kDa
ec_number	6.1.1.15
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4017

MAHHHHHHSNILGITSKKIENFSDWYTQVIVKSELIEYYDISGCYILRPAAYYIWECVQAFFNKEIKKLNVENSYFPLFVTKNKLEKEKNHIEGFSPEVAWVTKYGDSNLPEEIAIRPTSETIMYSVFPKWIRSYRDLPLKLNQWNTVVRWEFKQPTPFIRTREFLWQEGHTAHKNEEEAVKLVFDILDLYRRWYEEYLAVPIIKGIKSEGEKFGGANFTSTAEAFISENGRAIQAATSHYLGTNFAKMFKIEFEDENEVKQYVHQTSWGCTTRSIGIMIMTHGDDKGLVLPPNVSKYKVVIVPIFYKTTDENAIHSYCKDIEKILKNAQINCVYDDRASYSPGYKFNHWELRGIPIRIEVGPKDLQNNSCVIVRRDNNEKCNVKKESVLLETQQMLVDIHKNLFLKAKKKLDDSIVQVTSFSEVMNALNKKKMVLAPWCEDIATEEEIKKETQRLSLNQTNSETTLSGAMKPLCIPLDQPPMPPNMKCFWSGKPAKRWCLFGRSY

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	N-[(3M)-3-(4-aminothieno[3,2-d]pyrimidin-6-yl)benzene-1-sulfonyl]-L-prolinamide
formula_weight	403.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	8

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6. Citations (1)

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length_a	106.660 Å
length_b	106.660 Å
length_c	185.480 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	2.430 Å
resolution_low	46.230 Å
r_factor	0.2028
r_work	0.2013
r_free	0.2332

fit	/app/data/saxs_computation/yo/9yon/9yon.fit
pddf	/app/data/pr_computation/yo/9yon/9yon.pr.out
profile	/app/data/saxs_computation/yo/9yon/9yon.dat