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9z4d

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

Method: X-RAY DIFFRACTION D_max: 113.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z4d
deposition_date	2025-11-10
last_revision	2025-11-19
title	Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Hexagonal 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	32.46 Å
rg_electron	31.90 Å
i0	143119000.00
molecular_weight	99846.0 kDa
excluded_volume	126320 Å³
envelope_volume	148330 Å³
shell_volume	39656 Å³
envelope_diameter	117.5 Å
shell_rg	37.83 Å
envelope_rg	32.09 Å
shape_rg	31.92 Å
total_rg	32.29 Å
total_atoms	7053
n_residues	856
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	113.3 Å
rg_real	34.02 Å
rg_real_error	0.45 Å
i0_real	1.4340e+08
i0_real_error	2.0070e+06
rg_reciprocal	32.58 Å
i0_reciprocal	143100000.0000
total_estimate	0.6555
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	34.7 Å
skewness	0.560
kurtosis	-0.208
angular_range	— – 0.2450 Å⁻¹
current_alpha	3.0310
highest_alpha	34480000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 0.882; Sysdev: 0.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.684

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	7055

MAHHHHHHMGTLEAQTQGPGSLPKWNQPSKEGKKITNLFVNNSLTHSKVEFIPQEGNKIKWYACGPTVYDAAHLGHARTYVSFDIIRRILVNYFKYDVFMVINITDIDDKIIKRSVEEKIGFTELARKWEYEFWEDMKSLNVLLPTAITRVSEYVGDIVKYIEKIIENKYAYVSEEGSVYFDIDEFKKSEKHFYARMEPLSVKDENKILEGEGDLGVISKKKKNAYDFALWKSSKPNEPHWDSPWGKGRPGWHIECSTMASNILGDVLDIHSGGIDLRFPHHDNELAQSEAFFDHSQWVNYFLHSGHLHIEGLKMSKSLKNFITIKNMLTKYTSNQIRILFLLNKWDNFMNYSPNGESMVQCIEIDKSFTNFFAIILMKIKNFDLNSCNLYWSDADNKLNLLFRQTKNKIHEHFLDNFNTPDALLAIQKLITEINIYMDKEKIQIGLLLEIKHYINFIFDTFGLIY

Source

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

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2

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6. Citations (1)

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length_a	120.174 Å
length_b	120.174 Å
length_c	363.170 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	2.870 Å
resolution_low	47.810 Å
r_factor	0.2164
r_work	0.2154
r_free	0.2360

fit	/app/data/saxs_computation/z4/9z4d/9z4d.fit
pddf	/app/data/pr_computation/z4/9z4d/9z4d.pr.out
profile	/app/data/saxs_computation/z4/9z4d/9z4d.dat