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9yt3

;Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with 5'-Sulfamoyladenosine ;

Method: X-RAY DIFFRACTION D_max: 112.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yt3
deposition_date	2025-10-20
last_revision	2025-10-29
title	;Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with 5'-Sulfamoyladenosine ;
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	32.53 Å
rg_electron	32.09 Å
i0	154353000.00
molecular_weight	102100.0 kDa
excluded_volume	128440 Å³
envelope_volume	151780 Å³
shell_volume	40222 Å³
envelope_diameter	122.1 Å
shell_rg	38.06 Å
envelope_rg	32.39 Å
shape_rg	32.12 Å
total_rg	32.44 Å
total_atoms	7177
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	112.1 Å
rg_real	32.74 Å
rg_real_error	1.29 Å
i0_real	1.5440e+08
i0_real_error	3.0370e+06
rg_reciprocal	32.65 Å
i0_reciprocal	154300000.0000
total_estimate	0.8461
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.6 Å
skewness	0.516
kurtosis	-0.218
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	40880000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.728; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.903

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

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	7202

MAHHHHHHMGTLEAQTQGPGSLPKWNQPSKEGKKITNLFVNNSLTHSKVEFIPQEGNKIKWYACGPTVYDAAHLGHARTYVSFDIIRRILVNYFKYDVFMVINITDIDDKIIKRSVEEKIGFTELARKWEYEFWEDMKSLNVLLPTAITRVSEYVGDIVKYIEKIIENKYAYVSEEGSVYFDIDEFKKSEKHFYARMEPLSVKDENKILEGEGDLGVISKKKKNAYDFALWKSSKPNEPHWDSPWGKGRPGWHIECSTMASNILGDVLDIHSGGIDLRFPHHDNELAQSEAFFDHSQWVNYFLHSGHLHIEGLKMSKSLKNFITIKNMLTKYTSNQIRILFLLNKWDNFMNYSPNGESMVQCIEIDKSFTNFFAIILMKIKNFDLNSCNLYWSDADNKLNLLFRQTKNKIHEHFLDNFNTPDALLAIQKLITEINIYMDKEKIQIGLLLEIKHYINFIFDTFGLIY

Source

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

Entity 2 non-polymer

description	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE
formula_weight	346.3 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	24

Entity 6 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	17

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6. Citations (1)

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length_a	121.070 Å
length_b	121.070 Å
length_c	364.871 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	2.770 Å
resolution_low	50.390 Å
r_factor	0.1912
r_work	0.1890
r_free	0.2335

fit	/app/data/saxs_computation/yt/9yt3/9yt3.fit
pddf	/app/data/pr_computation/yt/9yt3/9yt3.pr.out
profile	/app/data/saxs_computation/yt/9yt3/9yt3.dat