← Back to search

9wqt

Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with reveromycin A and isoleucine

Method: X-RAY DIFFRACTION D_max: 124.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9wqt
deposition_date	2025-09-11
last_revision	2026-04-08
title	Crystal structure of Saccharomyces cerevisiae isoleucyl-tRNA synthetase in complex with reveromycin A and isoleucine
keywords	isoleucyl-tRNA synthetase, reveromycin, LIGASE; LIGASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	37.18 Å
rg_electron	36.98 Å
i0	159265000.00
molecular_weight	105940.0 kDa
excluded_volume	134120 Å³
envelope_volume	177130 Å³
shell_volume	42128 Å³
envelope_diameter	125.6 Å
shell_rg	40.96 Å
envelope_rg	36.75 Å
shape_rg	36.93 Å
total_rg	37.42 Å
total_atoms	7493
n_residues	919
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

▼

3. P(r) Analysis (GNOM)

dmax	124.1 Å
rg_real	37.40 Å
rg_real_error	1.06 Å
i0_real	1.5930e+08
i0_real_error	2.7360e+06
rg_reciprocal	37.27 Å
i0_reciprocal	159200000.0000
total_estimate	0.6645
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	34.6 Å
skewness	0.396
kurtosis	-0.635
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	31110000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.781; Smooth: 0.902

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Isoleucine--tRNA ligase, cytoplasmic
formula_weight	113864.7 kDa
ec_number	6.1.1.5
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8157

MSESNAHFSFPKEEEKVLSLWDEIDAFHTSLELTKDKPEFSFFDGPPFATGTPHYGHILASTIKDIVPRYATMTGHHVERRFGWDTHGVPIEHIIDKKLGITGKDDVFKYGLENYNNECRSIVMTYASDWRKTIGRLGRWIDFDNDYKTMYPSFMESTWWAFKQLHEKGQVYRGFKVMPYSTGLTTPLSNFEAQQNYKDVNDPAVTIGFNVIGQEKTQLVAWTTTPWTLPSNLSLCVNADFEYVKIYDETRDRYFILLESLIKTLYKKPKNEKYKIVEKIKGSDLVGLKYEPLFPYFAEQFHETAFRVISDDYVTSDSGTGIVHNAPAFGEEDNAACLKNGVISEDSVLPNAIDDLGRFTKDVPDFEGVYVKDADKLIIKYLTNTGNLLLASQIRHSYPFCWRSDTPLLYRSVPAWFVRVKNIVPQMLDSVMKSHWVPNTIKEKRFANWIANARDWNVSRNRYWGTPIPLWVSDDFEEVVCVGSIKELEELTGVRNITDLHRDVIDKLTIPSKQGKGDLKRIEEVFDCWFESGSMPYASQHYPFENTEKFDERVPANFISEGLDQTRGWFYTLAVLGTHLFGSVPYKNVIVSGIVLAADGRKMSKSLKNYPDPSIVLNKYGADALRLYLINSPVLKAESLKFKEEGVKEVVSKVLLPWWNSFKFLDGQIALLKKMSNIDFQYDDSVKSDNVMDRWILASMQSLVQFIHEEMGQYKLYTVVPKLLNFIDELTNWYIRFNRRRLKGENGVEDCLKALNSLFDALFTFVRAMAPFTPFLSESIYLRLKEYIPEAVLAKYGKDGRSVHFLSYPVVKKEYFDEAIETAVSRMQSVIDLGRNIREKKTISLKTPLKTLVILHSDESYLKDVEALKNYIIEELNVRDVVITSDEAKYGVEYKAVADWPVLGKKLKKDAKKVKDALPSVTSEQVREYLESGKLEVAGIELVKGDLNAIRGLPESAVQAGQETRTDQDVLIIMDTNIYSELKSHHHHHH

Source

organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
common_name	;Baker's yeast ;
ncbi_taxonomy_id	559292
host_organism	Escherichia coli

Entity 2 non-polymer

description	ISOLEUCINE
formula_weight	131.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	;(2E,4S,5S,6E,8E)-10-[(2S,3R,6S,8R,9S)-3-butyl-9-methyl-2-[(1E,3E)-3-methyl-5-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-3-(4-oxidanyl-4-oxidanylidene-butanoyl)oxy-1,7-dioxaspiro[5.5]undecan-8-yl]-4,8-dimethyl-5-oxidanyl-deca-2,6,8-trienoic acid ;
formula_weight	660.8 kDa
src_method	nat
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	608

▶

6. Citations (1)

▶

length_a	170.811 Å
length_b	65.042 Å
length_c	142.109 Å
angle_alpha	90.00 °
angle_beta	107.79 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.900 Å
resolution_low	47.880 Å
r_factor	0.1943
r_work	0.1930
r_free	0.2195

fit	/app/data/saxs_computation/wq/9wqt/9wqt.fit
pddf	/app/data/pr_computation/wq/9wqt/9wqt.pr.out
profile	/app/data/saxs_computation/wq/9wqt/9wqt.dat