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9sh9

Thermus thermophilus asparaginyl-tRNA synthetase dimer with bound ATP

Method: X-RAY DIFFRACTION D_max: 103.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sh9
deposition_date	2025-08-25
last_revision	2025-09-17
title	Thermus thermophilus asparaginyl-tRNA synthetase dimer with bound ATP
keywords	RNA binding protein Enzyme, synthetises asparaginyl-adenylate from asparagine and ATP, TRANSLATION; TRANSLATION
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	30.00 Å
rg_electron	29.06 Å
i0	165634000.00
molecular_weight	101730.0 kDa
excluded_volume	126920 Å³
envelope_volume	153380 Å³
shell_volume	42657 Å³
envelope_diameter	109.3 Å
shell_rg	37.44 Å
envelope_rg	29.63 Å
shape_rg	29.06 Å
total_rg	29.79 Å
total_atoms	7186
n_residues	866
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	103.4 Å
rg_real	29.92 Å
rg_real_error	0.77 Å
i0_real	1.6560e+08
i0_real_error	2.8060e+06
rg_reciprocal	29.95 Å
i0_reciprocal	165600000.0000
total_estimate	0.7956
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.1 Å
skewness	0.290
kurtosis	-0.316
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	53680000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Asparagine--tRNA ligase
formula_weight	50858.9 kDa
ec_number	6.1.1.22
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7203

MRVFIDEIARHVDQEVELRGWLYQRRSKGKIHFLILRDGTGFLQATVVQGEVPEAVFREADHLPQETALRVWGRVREDRRAPGGFELAVRDLQVVSRPQGEYPIGPKEHGIDFLMDHRHLWLRHRRPFAVMRIRDELERAIHEFFGERGFLRFDAPILTPSAVEGTTELFEVELFDGEKAYLSQSGQLYAEAGALAFAKVYTFGPTFRAERSKTRRHLLEFWMVEPEVAFMTHEENMALQEELVSFLVARVLERRSRELEMLGRDPKALEPAAEGHYPRLTYKEAVALVNRIAQEDPEVPPLPYGEDFGAPHEAALSRRFDRPVFVERYPARIKAFYMEPDPEDPELVLNDDLLAPEGYGEIIGGSQRIHDLELLRRKIQEFGLPEEVYDWYLDLRRFGSVPHSGFGLGLERTVAWICGLAHVREAIPFPRMYTRMRP

Source

organism	Thermus thermophilus HB8
ncbi_taxonomy_id	300852
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6

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6. Citations (3)

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length_a	124.954 Å
length_b	124.954 Å
length_c	246.821 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 65 2 2
int_tables_number	179
crystal_system	—

resolution	2.950 Å
resolution_low	24.474 Å
r_factor	—
r_work	0.2039
r_free	0.2275

fit	/app/data/saxs_computation/sh/9sh9/9sh9.fit
pddf	/app/data/pr_computation/sh/9sh9/9sh9.pr.out
profile	/app/data/saxs_computation/sh/9sh9/9sh9.dat

Thermus thermophilus asparaginyl-tRNA synthetase dimer with bound ATP

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