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9sfq

Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type tRNATyr(GUC).

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sfq
deposition_date	2025-08-20
title	Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type tRNATyr(GUC).
keywords	aminoacyl-tRNA synthetase, ligase, aminoacyl-adenylate, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	30.03 Å
rg_electron	29.32 Å
i0	154733000.00
molecular_weight	78127.0 kDa
excluded_volume	88811 Å³
envelope_volume	124590 Å³
shell_volume	35562 Å³
envelope_diameter	95.6 Å
shell_rg	36.44 Å
envelope_rg	28.72 Å
shape_rg	28.93 Å
total_rg	30.76 Å
total_atoms	9919
n_residues	503
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	29.92 Å
rg_real_error	0.61 Å
i0_real	1.5470e+08
i0_real_error	2.3310e+06
rg_reciprocal	29.97 Å
i0_reciprocal	154700000.0000
total_estimate	0.9122
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	40.4 Å
skewness	0.128
kurtosis	-0.622
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	11670000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.956

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Tyrosine--tRNA ligase
formula_weight	48786.2 kDa
ec_number	6.1.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10879

MAGTGHTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQFQELGHKVVLIIGDFTGMIGDPSGRSKTRPPLTLEETRENAKTYVAQAGKILRQEPHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGIPISLHELLYPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYDEVAKGGIPEEIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFVRVRLSD

Source

organism	Thermus thermophilus HB27
ncbi_taxonomy_id	262724
host_organism	Escherichia coli

Entity 2 polymer

description	Wild-type, fully modified Thermus thermopilus tRNATyr(GUC)
formula_weight	27922.9 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	T

GGGCAGGUGCCCGAGCGGCCAAAGGGGACGGUCUGUAAAACCGUUGGCGUAUGCCUUCGCUGGUUCGAAUCCAGCCCUGCCCACCA

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	10

Entity 5 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	571

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6. Citations (1)

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length_a	124.319 Å
length_b	67.546 Å
length_c	111.169 Å
angle_alpha	90.00 °
angle_beta	110.21 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.890 Å
resolution_low	29.500 Å
r_factor	0.1746
r_work	0.1728
r_free	0.2087

fit	/app/data/saxs_computation/sf/9sfq/9sfq.fit
pddf	/app/data/pr_computation/sf/9sfq/9sfq.pr.out
profile	/app/data/saxs_computation/sf/9sfq/9sfq.dat

Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type tRNATyr(GUC).

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

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)