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1bbu

LYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE

Method: X-RAY DIFFRACTION D_max: 95.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1bbu
deposition_date	1998-04-24
title	LYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE
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	29.68 Å
rg_electron	29.00 Å
i0	49068600.00
molecular_weight	53900.0 kDa
excluded_volume	67093 Å³
envelope_volume	88594 Å³
shell_volume	27098 Å³
envelope_diameter	99.9 Å
shell_rg	34.40 Å
envelope_rg	28.97 Å
shape_rg	29.02 Å
total_rg	29.48 Å
total_atoms	3799
n_residues	486
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	95.8 Å
rg_real	29.86 Å
rg_real_error	0.72 Å
i0_real	4.9070e+07
i0_real_error	7.3490e+05
rg_reciprocal	29.79 Å
i0_reciprocal	49070000.0000
total_estimate	0.8638
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.1 Å
skewness	0.434
kurtosis	-0.591
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	7971000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.857

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	PROTEIN (LYSYL-TRNA SYNTHETASE)
formula_weight	57546.1 kDa
ec_number	6.1.1.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3950

SEQHAQGADAVVDLNNELKTRREKLANLREQGIAFPNDFRRDHTSDQLHAEFDGKENEELEALNIEVAVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDDLPEGVYNEQFKKWDLGDILGAKGKLFKTKTGELSIHCTELRLLTKALRPLPDKFHGLQDQEARYRQRYLDLISNDESRNTFKVRSQILSGIRQFMVNRGFMEVETPMMQVIPGGAAARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELYMAYADYKDLIELTESLFRTLAQDILGKTEVTYGDVTLDFGKPFEKLTMREAIKKYRPETDMADLDNFDSAKAIAESIGIHVEKSWGLGRIVTEIFEEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAQRFLDQVAAKDAGDDEAMFYDEDYVTALEHGLPPTAGLGIGIDRMVMLFTNSHTIRDVILFPAMRPVK

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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	151

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6. Citations (3)

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length_a	181.820 Å
length_b	181.820 Å
length_c	93.070 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	2.700 Å
resolution_low	20.000 Å
r_factor	0.2280
r_work	0.2280
r_free	0.2970

fit	/app/data/saxs_computation/bb/1bbu/1bbu.fit
pddf	/app/data/pr_computation/bb/1bbu/1bbu.pr.out
profile	/app/data/saxs_computation/bb/1bbu/1bbu.dat

LYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE

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