SAXSdb — 1e4m

▼

1. Structure Basics

entry_id	1e4m
deposition_date	2000-07-10
title	MYROSINASE FROM SINAPIS ALBA
keywords	HYDROLASE, FAMILY 1 GLYCOSYL HYDROLASE, GLUCOSINOLATE, TIM BARREL; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	23.71 Å
rg_electron	22.29 Å
i0	64390200.00
molecular_weight	61722.0 kDa
excluded_volume	76450 Å³
envelope_volume	87231 Å³
shell_volume	30903 Å³
envelope_diameter	78.4 Å
shell_rg	30.65 Å
envelope_rg	22.81 Å
shape_rg	22.21 Å
total_rg	23.38 Å
total_atoms	4337
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

▼

3. P(r) Analysis (GNOM)

dmax	70.6 Å
rg_real	23.50 Å
rg_real_error	0.10 Å
i0_real	6.2120e+07
i0_real_error	6.5450e+05
rg_reciprocal	23.57 Å
i0_reciprocal	64390000.0000
total_estimate	0.7022
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	30.9 Å
skewness	0.121
kurtosis	-0.380
angular_range	— – 0.3350 Å⁻¹
current_alpha	7.9270
highest_alpha	12980000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 0.916; Sysdev: 0.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.631

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (9)

Entity 1 polymer

description	MYROSINASE MA1
formula_weight	57078.3 kDa
ec_number	3.2.1.147
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M
atom_count	5201

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)][alpha-D-mannopyranose-(1-6)]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	1189.1 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	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	8

Entity 8 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	797

▶

6. Citations (2)

▶

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	1.200 Å
resolution_low	10.000 Å
r_factor	—
r_work	0.1240
r_free	0.1420

fit	/app/data/saxs_computation/e4/1e4m/1e4m.fit
pddf	/app/data/pr_computation/e4/1e4m/1e4m.pr.out
profile	/app/data/saxs_computation/e4/1e4m/1e4m.dat

MYROSINASE FROM SINAPIS ALBA

SAXS Profile

P(r) Distribution