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9qw7

The crystal structure of the adenyly transferase domain of Candida glabrata tRNA ligase

Method: X-RAY DIFFRACTION D_max: 122.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qw7
deposition_date	2025-04-14
title	The crystal structure of the adenyly transferase domain of Candida glabrata tRNA ligase
keywords	tRNA ligase, LIGASE; LIGASE
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	32.88 Å
rg_electron	33.27 Å
i0	119115000.00
molecular_weight	86786.0 kDa
excluded_volume	108490 Å³
envelope_volume	144120 Å³
shell_volume	38351 Å³
envelope_diameter	131.4 Å
shell_rg	37.15 Å
envelope_rg	33.46 Å
shape_rg	33.26 Å
total_rg	33.65 Å
total_atoms	6113
n_residues	745
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	122.5 Å
rg_real	33.24 Å
rg_real_error	1.45 Å
i0_real	1.1910e+08
i0_real_error	2.1550e+06
rg_reciprocal	33.09 Å
i0_reciprocal	119100000.0000
total_estimate	0.7989
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.7 Å
skewness	0.653
kurtosis	0.201
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	28160000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.581; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.748; Smooth: 0.891

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	tRNA ligase
formula_weight	44630.2 kDa
ec_number	6.5.1.3
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6146

MNLSRNVKDLVEKLEAASQLPGRGKAIKRICKLSNSDGQVVSWKFNEWDYGKNNIKLPCCARGLFITDDSKNPQIVARGYDKFFNIDETPFTRWDTLESDTKGTYNVTLKANGCIIFVSGMADGTLVVCSKHSTGPRDDVDRNHADAGEQFLLSQLKSIGIEPQQLALELYQNNVTAVAEYCDDTFEEHILEYTNDDVGLYLHGINYNETTFRTWDMDSVSEFARKYNFKQIKYENFNDFTLLKKFLEECSNSGTYHGQEVEGFVIRCKTRENGNDFFFKYKFEEPYLMYRQWREVTKDYISTKSRVFKFKKHKFITNKYLDFVIPILDSSPALCEEYMKGFGIIKLRNEFLKDFGMSGLEILNHEKVLELENANKIDYDTVDE

Source

organism	Nakaseomyces glabratus
ncbi_taxonomy_id	5478
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	33

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6. Citations (1)

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length_a	81.796 Å
length_b	81.796 Å
length_c	286.593 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.750 Å
resolution_low	63.500 Å
r_factor	0.2198
r_work	0.2177
r_free	0.2625

fit	/app/data/saxs_computation/qw/9qw7/9qw7.fit
pddf	/app/data/pr_computation/qw/9qw7/9qw7.pr.out
profile	/app/data/saxs_computation/qw/9qw7/9qw7.dat

The crystal structure of the adenyly transferase domain of Candida glabrata tRNA ligase

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