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1e24

LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine and ATP and MN2+

Method: X-RAY DIFFRACTION D_max: 94.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e24
deposition_date	2000-05-16
title	LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine and ATP and MN2+
keywords	LIGASE, AMINOACYL-TRNA SYNTHETASE, PROTEIN BIOSYNTHESIS; LIGASE
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	29.28 Å
rg_electron	28.75 Å
i0	53075900.00
molecular_weight	55933.0 kDa
excluded_volume	69527 Å³
envelope_volume	88520 Å³
shell_volume	27222 Å³
envelope_diameter	99.4 Å
shell_rg	34.24 Å
envelope_rg	28.77 Å
shape_rg	28.79 Å
total_rg	29.17 Å
total_atoms	3927
n_residues	485
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	94.5 Å
rg_real	29.47 Å
rg_real_error	0.78 Å
i0_real	5.3080e+07
i0_real_error	8.1720e+05
rg_reciprocal	29.39 Å
i0_reciprocal	53070000.0000
total_estimate	0.6478
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.446
kurtosis	-0.592
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	11580000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 0.092; Positv: 1.000; Valcen: 0.855; Smooth: 0.853

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	LYSYL-TRNA SYNTHETASE
formula_weight	57767.2 kDa
ec_number	6.1.1.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4287

SEQETRGANEAIDFNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVEKSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRPQK

Source

organism	ESCHERICHIA COLI
ncbi_taxonomy_id	83333
host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

description	LYSINE
formula_weight	147.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	360

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6. Citations (1)

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length_a	143.600 Å
length_b	143.600 Å
length_c	177.230 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	2.350 Å
resolution_low	25.000 Å
r_factor	0.1820
r_work	0.1820
r_free	0.2490

fit	/app/data/saxs_computation/e2/1e24/1e24.fit
pddf	/app/data/pr_computation/e2/1e24/1e24.pr.out
profile	/app/data/saxs_computation/e2/1e24/1e24.dat