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9u98

Glycoside hydrolase family 1 beta-glucosidase (E318G mutant) from Streptomyces griseus (sophorose complex)

Method: X-RAY DIFFRACTION D_max: 114.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u98
deposition_date	2025-03-27
title	Glycoside hydrolase family 1 beta-glucosidase (E318G mutant) from Streptomyces griseus (sophorose complex)
keywords	beta-Glucosidase, HYDROLASE; 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	37.86 Å
rg_electron	37.23 Å
i0	475973000.00
molecular_weight	174060.0 kDa
excluded_volume	215710 Å³
envelope_volume	268380 Å³
shell_volume	58416 Å³
envelope_diameter	128.3 Å
shell_rg	44.59 Å
envelope_rg	36.91 Å
shape_rg	37.20 Å
total_rg	37.72 Å
total_atoms	12307
n_residues	1560
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	114.5 Å
rg_real	37.62 Å
rg_real_error	0.91 Å
i0_real	4.7600e+08
i0_real_error	8.8830e+06
rg_reciprocal	37.77 Å
i0_reciprocal	476000000.0000
total_estimate	0.8309
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	57.2 Å
skewness	0.043
kurtosis	-0.672
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	681900000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Putative beta-glucosidase
formula_weight	45690.6 kDa
mutation	E318G
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	12837

MTHTPAWDQKTPVPFPEGFLWGASTAAHQIEGNNTDSDWWVKEHAAGTHIAEPSLDACDSYHRWPEDMDLLASLGFTDYRFSVEWARIEPVEGHFSRAQLAHYRRMVEGAIERGLRPMVTLHHFTVPQWFEARGGWTAEGAVELFARYVAACAPVISEGVSHVCTINEPNMIAVMAGQAKRGDNSFPPAGLPTPDDETTAAVIAAHHAAVKEVRALDAGIQVGWTIANQVYQALPGAEDVTAAYRHPREDVFIEAARGDDWIGVQSYTRTRIGPEGPIPAADDVERTLTTWEYYPTAVGEALRHTAAVVGDVPLIVTGNGIATADDSRRVDYYAGALDEVASALADGLDIRGYLAWSALDNYEWGTYKATFGLIAIDWETFERTPRDSAKWLGSLGRTRELPRTAALEHHHHHH

Source

organism	Streptomyces griseus subsp. griseus NBRC 13350
ncbi_taxonomy_id	455632
host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

description	beta-D-glucopyranose-(1-2)-beta-D-glucopyranose
formula_weight	342.3 kDa
src_method	man
entity_count	2

Entity 3 branched

description	beta-D-glucopyranose-(1-2)-alpha-D-glucopyranose
formula_weight	342.3 kDa
src_method	man
entity_count	3

Entity 4 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

description	beta-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	530

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6. Citations (1)

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length_a	91.793 Å
length_b	100.179 Å
length_c	96.048 Å
angle_alpha	90.00 °
angle_beta	102.87 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.130 Å
resolution_low	46.818 Å
r_factor	—
r_work	0.1808
r_free	0.2278

fit	/app/data/saxs_computation/u9/9u98/9u98.fit
pddf	/app/data/pr_computation/u9/9u98/9u98.pr.out
profile	/app/data/saxs_computation/u9/9u98/9u98.dat