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9sdf

;Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type modified tRNA(Tyr), tyrosine and AMP ;

Method: X-RAY DIFFRACTION D_max: 92.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sdf
deposition_date	2025-08-13
title	;Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type modified tRNA(Tyr), tyrosine and AMP ;
keywords	aminoacyl-tRNA synthetase, ligase, tRNA, 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	29.68 Å
rg_electron	29.02 Å
i0	154910000.00
molecular_weight	78217.0 kDa
excluded_volume	88853 Å³
envelope_volume	122090 Å³
shell_volume	35028 Å³
envelope_diameter	93.6 Å
shell_rg	36.27 Å
envelope_rg	28.62 Å
shape_rg	28.63 Å
total_rg	30.45 Å
total_atoms	9914
n_residues	506
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	92.8 Å
rg_real	29.58 Å
rg_real_error	0.63 Å
i0_real	1.5490e+08
i0_real_error	2.3020e+06
rg_reciprocal	29.62 Å
i0_reciprocal	154900000.0000
total_estimate	0.9125
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	38.5 Å
skewness	0.148
kurtosis	-0.617
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	11150000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.968

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

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	10714

MAGTGHTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQFQELGHKVVLIIGDFTGMIGDPSGRSKTRPPLTLEETRENAKTYVAQAGKILRQEPHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGIPISLHELLYPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYDEVAKGGIPEEIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFVRVRLSD

Source

organism	Thermus thermophilus HB27
ncbi_taxonomy_id	262724
host_organism	Escherichia coli

Entity 2 polymer

description	Thermus thermophilus tRNA(Tyr)(GUA) (86-MER)
formula_weight	27923.9 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	T

GGGCAGGUGCCCGAGUGGCCAAAGGGGACGGUCUGUAAAACCGUUGGCGUAUGCCUUCGCUGGUUCGAAUCCAGCCCUGCCCACCA

Entity 3 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	TYROSINE
formula_weight	181.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	5

Entity 8 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	497

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6. Citations (1)

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length_a	125.067 Å
length_b	67.378 Å
length_c	113.817 Å
angle_alpha	90.00 °
angle_beta	112.25 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.900 Å
resolution_low	16.740 Å
r_factor	0.1890
r_work	0.1880
r_free	0.2139

fit	/app/data/saxs_computation/sd/9sdf/9sdf.fit
pddf	/app/data/pr_computation/sd/9sdf/9sdf.pr.out
profile	/app/data/saxs_computation/sd/9sdf/9sdf.dat

;Structure at 1.9 A resolution of Thermus thermophilus tyrosyl-tRNA synthetase bound to wild-type modified tRNA(Tyr), tyrosine and AMP ;

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 (10)

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 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)