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1e72

Myrosinase from Sinapis alba with bound gluco-hydroximolactam and sulfate or ascorbate

Method: X-RAY DIFFRACTION D_max: 82.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e72
deposition_date	2000-08-23
title	Myrosinase from Sinapis alba with bound gluco-hydroximolactam and sulfate or ascorbate
keywords	HYDROLASE, FAMILY 1 GLYCOSYL HYDROLASE, GLUCOSINOLATE, TIM BARREL, ACTIVATION, INHIBITOR, TRANSITION STATE ANALOGUE; HYDROLASE
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	23.62 Å
rg_electron	22.20 Å
i0	64555300.00
molecular_weight	61739.0 kDa
excluded_volume	76480 Å³
envelope_volume	86919 Å³
shell_volume	30856 Å³
envelope_diameter	78.3 Å
shell_rg	30.59 Å
envelope_rg	22.74 Å
shape_rg	22.12 Å
total_rg	23.30 Å
total_atoms	4340
n_residues	499
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	82.1 Å
rg_real	23.44 Å
rg_real_error	0.60 Å
i0_real	6.4560e+07
i0_real_error	8.7720e+05
rg_reciprocal	23.49 Å
i0_reciprocal	64560000.0000
total_estimate	0.7659
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	30.8 Å
skewness	0.117
kurtosis	-0.399
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	14350000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.661; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	MYROSINASE MA1
formula_weight	57078.3 kDa
ec_number	3.2.3.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M
atom_count	5204

DEEITCQENLPFTCGNTDALNSSSFSSDFIFGVASSAYQIEGTIGRGLNIWDGFTHRYPNKSGPDHGNGDTTCDSFSYWQKDIDVLDELNATGYRFSIAWSRIIPRGKRSRGVNEKGIDYYHGLISGLIKKGITPFVTLFHWDLPQTLQDEYEGFLDPQIIDDFKDYADLCFEEFGDSVKYWLTINQLYSVPTRGYGSALDAPGRCSPTVDPSCYAGNSSTEPYIVAHHQLLAHAKVVDLYRKNYTHQGGKIGPTMITRWFLPYNDTDRHSIAATERMKEFFLGWFMGPLTNGTYPQIMIDTVGERLPSFSPEESNLVKGSYDFLGLNYYFTQYAQPSPNPVNSTNHTAMMDAGAKLTYINASGHYIGPLFEKDKADSTDNIYYYPKGIYSVMDYFKNKYYNPLIYVTENGISTPGDENRNQSMLDYTRIDYLCSHLCFLNKVIKEKDVNVKGYLAWALGDNYEFNKGFTVRFGLSYIDWNNVTDRDLKKSGQWYQSFISP

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 3 branched

description	;beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	864.8 kDa
src_method	man
entity_count	1

Entity 4 branched

description	;beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1026.9 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	6

Entity 6 non-polymer

description	ASCORBIC ACID
formula_weight	176.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	(2S,3S,4R,5R)-6-(HYDROXYAMINO)-2-(HYDROXYMETHYL)-2,3,4,5-TETRAHYDROPYRIDINE-3,4,5-TRIOL
formula_weight	192.2 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	8

Entity 10 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	787

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6. Citations (2)

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length_a	135.300 Å
length_b	137.200 Å
length_c	80.600 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	1.600 Å
resolution_low	10.000 Å
r_factor	—
r_work	0.1290
r_free	0.1570

fit	/app/data/saxs_computation/e7/1e72/1e72.fit
pddf	/app/data/pr_computation/e7/1e72/1e72.pr.out
profile	/app/data/saxs_computation/e7/1e72/1e72.dat