← Back to search

1exd

CRYSTAL STRUCTURE OF A TIGHT-BINDING GLUTAMINE TRNA BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE

Method: X-RAY DIFFRACTION D_max: 103.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1exd
deposition_date	2000-05-02
title	CRYSTAL STRUCTURE OF A TIGHT-BINDING GLUTAMINE TRNA BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE
keywords	engineered tRNA, tRNA-protein complex, tRNA aptamer, ligase-RNA COMPLEX; ligase/RNA
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.45 Å
rg_electron	30.62 Å
i0	168724000.00
molecular_weight	84925.0 kDa
excluded_volume	98108 Å³
envelope_volume	124820 Å³
shell_volume	35376 Å³
envelope_diameter	108.5 Å
shell_rg	36.24 Å
envelope_rg	30.57 Å
shape_rg	30.63 Å
total_rg	31.00 Å
total_atoms	5872
n_residues	602
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

▼

3. P(r) Analysis (GNOM)

dmax	103.2 Å
rg_real	30.50 Å
rg_real_error	0.75 Å
i0_real	1.6870e+08
i0_real_error	2.7730e+06
rg_reciprocal	30.48 Å
i0_reciprocal	168700000.0000
total_estimate	0.8829
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.7 Å
skewness	0.388
kurtosis	-0.340
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	13550000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.961

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	GLUTAMINE TRNA APTAMER
formula_weight	23528.0 kDa
mutation	44-CAUUC-48 TO 44-AGGU-48
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B
atom_count	6031

GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGAGGUCGAGGUUCGAAUCCUCGUACCCCAGCCA

Entity 2 polymer

description	GLUTAMINYL-TRNA SYNTHETASE
formula_weight	62894.1 kDa
ec_number	6.1.1.18
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYVDELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYQGEGEMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPNPGAADDFLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPVFNRTVGLRDT

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	159

▶

6. Citations (1)

▶

length_a	236.940 Å
length_b	93.980 Å
length_c	113.910 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.700 Å
resolution_low	6.000 Å
r_factor	—
r_work	0.2160
r_free	0.2890

fit	/app/data/saxs_computation/ex/1exd/1exd.fit
pddf	/app/data/pr_computation/ex/1exd/1exd.pr.out
profile	/app/data/saxs_computation/ex/1exd/1exd.dat

CRYSTAL STRUCTURE OF A TIGHT-BINDING GLUTAMINE TRNA BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)