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1efw

Crystal structure of aspartyl-tRNA synthetase from Thermus thermophilus complexed to tRNAasp from Escherichia coli

Method: X-RAY DIFFRACTION D_max: 128.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1efw
deposition_date	2000-02-10
title	Crystal structure of aspartyl-tRNA synthetase from Thermus thermophilus complexed to tRNAasp from Escherichia coli
keywords	ASPARTYL-TRNA SYNTHETASE, TRNA, PROTEIN-RNA COMPLEX, LIGASE/RNA, LIGASE-RNA complex; LIGASE/RNA
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	41.22 Å
rg_electron	39.06 Å
i0	675441000.00
molecular_weight	179720.0 kDa
excluded_volume	210930 Å³
envelope_volume	288520 Å³
shell_volume	62029 Å³
envelope_diameter	130.9 Å
shell_rg	44.70 Å
envelope_rg	38.73 Å
shape_rg	38.94 Å
total_rg	39.66 Å
total_atoms	12476
n_residues	1286
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	128.8 Å
rg_real	41.16 Å
rg_real_error	1.11 Å
i0_real	6.7540e+08
i0_real_error	1.1370e+07
rg_reciprocal	41.22 Å
i0_reciprocal	675500000.0000
total_estimate	0.8365
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	50.9 Å
skewness	0.248
kurtosis	-0.474
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	25560000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	ASPARTYL-TRNA
formula_weight	23724.3 kDa
src_method	man
entity_count	2

Polymer

type	polyribonucleotide
strand_id	C,D
atom_count	12572

GGAGCGGUAGUUCAGUCGGUUAGAAUACCUGCCUGUCACGCAGGGGGUCGCGGGUUCGAGUCCCGUCCGUUCC

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	ASPARTYL-TRNA SYNTHETASE
formula_weight	66124.8 kDa
ec_number	6.1.1.12
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

MRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP

Source

organism	Thermus thermophilus
ncbi_taxonomy_id	274
host_organism	Escherichia coli

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	96

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6. Citations (1)

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length_a	251.450 Å
length_b	251.450 Å
length_c	88.700 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63
int_tables_number	173
crystal_system	—

resolution	3.000 Å
resolution_low	15.000 Å
r_factor	0.2480
r_work	0.2480
r_free	0.2930

fit	/app/data/saxs_computation/ef/1efw/1efw.fit
pddf	/app/data/pr_computation/ef/1efw/1efw.pr.out
profile	/app/data/saxs_computation/ef/1efw/1efw.dat

Crystal structure of aspartyl-tRNA synthetase from Thermus thermophilus complexed to tRNAasp from Escherichia coli

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)