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9vci

Crystal structure of Escherichia coli tryptophanyl-tRNA synthetase in complex with an inhibitor

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vci
deposition_date	2025-06-06
last_revision	2025-09-24
title	Crystal structure of Escherichia coli tryptophanyl-tRNA synthetase in complex with an inhibitor
keywords	tryptophanyl-tRNA synthetase, an inhibitor, complex, LYASE; LYASE
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	30.66 Å
rg_electron	30.71 Å
i0	162850000.00
molecular_weight	67678.0 kDa
excluded_volume	65172 Å³
envelope_volume	109960 Å³
shell_volume	32426 Å³
envelope_diameter	118.3 Å
shell_rg	34.89 Å
envelope_rg	31.42 Å
shape_rg	30.67 Å
total_rg	31.03 Å
total_atoms	5110
n_residues	656
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	31.11 Å
rg_real_error	1.50 Å
i0_real	1.6290e+08
i0_real_error	2.8510e+06
rg_reciprocal	30.92 Å
i0_reciprocal	162800000.0000
total_estimate	0.7636
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.3 Å
skewness	0.737
kurtosis	0.133
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	37760000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.502; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.520; Smooth: 0.906

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Tryptophan--tRNA ligase
formula_weight	38373.7 kDa
ec_number	6.1.1.2
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5616

MTKPIVFSGAQPSGELTIGNYMGALRQWVNMQDDYHCIYCIVDQHAITVRQDAQKLRKATLDTLALYLACGIDPEKSTIFVQSHVPEHAQLGWALNCYTYFGELSRMTQFKDKSARYAENINAGLFDYPVLMAADILLYQTNLVPVGEDQKQHLELSRDIAQRFNALYGEIFKVPEPFIPKSGARVMSLLEPTKKMSKSDDNRNNVIGLLEDPKSVVKKIKRAVTDSDEPPVVRYDVQNKAGVSNLLDILSAVTGQSIPELEKQFEGKMYGHLKGEVADAVSGMLTELQERYHRFRNDEAFLQQVMKDGAEKASAHASRTLKAVYEAIGFVAKRHHHHHH

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	~{N}-[[5-[4-(6-azanyl-8-oxidanylidene-9-piperidin-4-yl-purin-7-yl)phenoxy]-2-fluoranyl-4-oxidanyl-phenyl]methyl]ethanamide
formula_weight	507.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	CHLORZOXAZONE
formula_weight	169.6 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	TRYPTOPHANYL-5'AMP
formula_weight	533.4 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	506

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6. Citations (1)

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length_a	61.495 Å
length_b	79.532 Å
length_c	77.651 Å
angle_alpha	90.00 °
angle_beta	105.82 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.880 Å
resolution_low	59.160 Å
r_factor	0.1950
r_work	0.1938
r_free	0.2183

fit	/app/data/saxs_computation/vc/9vci/9vci.fit
pddf	/app/data/pr_computation/vc/9vci/9vci.pr.out
profile	/app/data/saxs_computation/vc/9vci/9vci.dat