Crystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Orthrhombic P form)

Method: X-RAY DIFFRACTION D_max: 110.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yru
deposition_date	2025-10-17
last_revision	2025-10-29
title	Crystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Orthrhombic P form)
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	32.15 Å
rg_electron	31.20 Å
i0	128260000.00
molecular_weight	92153.0 kDa
excluded_volume	115670 Å³
envelope_volume	141970 Å³
shell_volume	38493 Å³
envelope_diameter	117.2 Å
shell_rg	37.48 Å
envelope_rg	31.88 Å
shape_rg	31.25 Å
total_rg	31.56 Å
total_atoms	6523
n_residues	840
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	110.8 Å
rg_real	32.35 Å
rg_real_error	1.23 Å
i0_real	1.2830e+08
i0_real_error	2.1880e+06
rg_reciprocal	32.27 Å
i0_reciprocal	128300000.0000
total_estimate	0.8457
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.2 Å
skewness	0.530
kurtosis	-0.168
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	32720000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.719; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.919

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	63.874 Å
length_b	104.024 Å
length_c	158.805 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	3.060 Å
resolution_low	49.770 Å
r_factor	0.2315
r_work	0.2285
r_free	0.2876

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

type	polypeptide(L)
strand_id	A,B
atom_count	6523

Crystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Orthrhombic P form)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

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

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

fit	/app/data/saxs_computation/yr/9yru/9yru.fit
pddf	/app/data/pr_computation/yr/9yru/9yru.pr.out
profile	/app/data/saxs_computation/yr/9yru/9yru.dat