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9yt0

Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with ADP (long soak)

Method: X-RAY DIFFRACTION D_max: 113.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yt0
deposition_date	2025-10-20
last_revision	2026-03-25
title	Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with ADP (long soak)
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Cysteinyl-tRNA synthetase, CysRS ;; TRANSFERASE
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	32.29 Å
rg_electron	31.85 Å
i0	154443000.00
molecular_weight	102230.0 kDa
excluded_volume	128690 Å³
envelope_volume	150030 Å³
shell_volume	40073 Å³
envelope_diameter	124.0 Å
shell_rg	38.00 Å
envelope_rg	32.12 Å
shape_rg	31.87 Å
total_rg	32.26 Å
total_atoms	7212
n_residues	859
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	113.8 Å
rg_real	32.49 Å
rg_real_error	1.12 Å
i0_real	1.5440e+08
i0_real_error	2.3020e+06
rg_reciprocal	32.41 Å
i0_reciprocal	154400000.0000
total_estimate	0.8433
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.8 Å
skewness	0.518
kurtosis	-0.203
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	35320000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.698; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.902; Smooth: 0.966

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Cysteine--tRNA ligase
formula_weight	54533.2 kDa
ec_number	6.1.1.16
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7296

MAHHHHHHMGTLEAQTQGPGSLPKWNQPSKEGKKITNLFVNNSLTHSKVEFIPQEGNKIKWYACGPTVYDAAHLGHARTYVSFDIIRRILVNYFKYDVFMVINITDIDDKIIKRSVEEKIGFTELARKWEYEFWEDMKSLNVLLPTAITRVSEYVGDIVKYIEKIIENKYAYVSEEGSVYFDIDEFKKSEKHFYARMEPLSVKDENKILEGEGDLGVISKKKKNAYDFALWKSSKPNEPHWDSPWGKGRPGWHIECSTMASNILGDVLDIHSGGIDLRFPHHDNELAQSEAFFDHSQWVNYFLHSGHLHIEGLKMSKSLKNFITIKNMLTKYTSNQIRILFLLNKWDNFMNYSPNGESMVQCIEIDKSFTNFFAIILMKIKNFDLNSCNLYWSDADNKLNLLFRQTKNKIHEHFLDNFNTPDALLAIQKLITEINIYMDKEKIQIGLLLEIKHYINFIFDTFGLIY

Source

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

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	76

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6. Citations (1)

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length_a	119.897 Å
length_b	119.897 Å
length_c	365.785 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	2.450 Å
resolution_low	47.770 Å
r_factor	0.1905
r_work	0.1891
r_free	0.2164

fit	/app/data/saxs_computation/yt/9yt0/9yt0.fit
pddf	/app/data/pr_computation/yt/9yt0/9yt0.pr.out
profile	/app/data/saxs_computation/yt/9yt0/9yt0.dat