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9sh8

Thermus thermophilus asparaginyl-tRNA synthetase with bound sulphamoyl-analogue of asparaginyl-adenylate (AsnAMS)

Method: X-RAY DIFFRACTION D_max: 93.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sh8
deposition_date	2025-08-25
last_revision	2025-09-17
title	Thermus thermophilus asparaginyl-tRNA synthetase with bound sulphamoyl-analogue of asparaginyl-adenylate (AsnAMS)
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	27.00 Å
rg_electron	26.41 Å
i0	44040300.00
molecular_weight	51257.0 kDa
excluded_volume	64065 Å³
envelope_volume	81115 Å³
shell_volume	26773 Å³
envelope_diameter	95.1 Å
shell_rg	32.48 Å
envelope_rg	26.76 Å
shape_rg	26.41 Å
total_rg	27.07 Å
total_atoms	3625
n_residues	438
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	93.1 Å
rg_real	27.17 Å
rg_real_error	0.75 Å
i0_real	4.4040e+07
i0_real_error	6.2340e+05
rg_reciprocal	27.12 Å
i0_reciprocal	44040000.0000
total_estimate	0.8474
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.8 Å
skewness	0.505
kurtosis	-0.286
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	10310000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.796; Smooth: 0.949

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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	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3678

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	1

Entity 3 non-polymer

description	5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE
formula_weight	461.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	42

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6. Citations (3)

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length_a	125.183 Å
length_b	125.183 Å
length_c	126.591 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 64 2 2
int_tables_number	181
crystal_system	—

resolution	2.620 Å
resolution_low	14.840 Å
r_factor	—
r_work	0.2090
r_free	0.2726

fit	/app/data/saxs_computation/sh/9sh8/9sh8.fit
pddf	/app/data/pr_computation/sh/9sh8/9sh8.pr.out
profile	/app/data/saxs_computation/sh/9sh8/9sh8.dat

Thermus thermophilus asparaginyl-tRNA synthetase with bound sulphamoyl-analogue of asparaginyl-adenylate (AsnAMS)

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