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9urg

Crystal structure of beta-glucosidase from Bacteroides ovatus bound to beta-D-Glucose

Method: X-RAY DIFFRACTION D_max: 110.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9urg
deposition_date	2025-04-29
last_revision	2026-05-20
title	Crystal structure of beta-glucosidase from Bacteroides ovatus bound to beta-D-Glucose
keywords	Glycosidase, beta-glucosidase, beta-D-glucose, 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	35.05 Å
rg_electron	34.30 Å
i0	416242000.00
molecular_weight	164660.0 kDa
excluded_volume	205590 Å³
envelope_volume	245790 Å³
shell_volume	57283 Å³
envelope_diameter	116.1 Å
shell_rg	42.82 Å
envelope_rg	34.54 Å
shape_rg	34.27 Å
total_rg	34.95 Å
total_atoms	11560
n_residues	1490
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	110.4 Å
rg_real	34.91 Å
rg_real_error	0.56 Å
i0_real	4.1620e+08
i0_real_error	6.7590e+06
rg_reciprocal	35.00 Å
i0_reciprocal	416300000.0000
total_estimate	0.8977
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.7 Å
skewness	0.207
kurtosis	-0.482
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0001
highest_alpha	90340000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.900

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	beta-glucosidase
formula_weight	89878.8 kDa
ec_number	3.2.1.21
mutation	H625Q
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12818

MASWSHPQFEKGSSHHHHHHSSGSGGGGGENLYFQGSNRDKINYNNMIYKKLSLSVLLFAAGFLTASAQKSPQDMDRFIDVLMNKMTLEEKIGQLNLPVTGEITTGQAKSSDIAAKIKKGEVGGLFNLKGVEKIREVQKQAVEDSRLGIPLLFGMDVIHGYETMFPIPLGLSCTWDMTAIEESARIAAVEASADGISWTFSPMVDISRDPRWGRVSEGSGEDPFLGAMIAEAMVRGYQGKNMERNDEIMACVKHFALYGAGEAGRDYNTVDMSRQRMFNDYMLPYEAAVEAGVGSVMASFNEVDGIPATANKWLMTDILRGQWGFNGFVVTDYTGISEMIDHGIGDLQTVSARAINAGVDMDMVSEGFVGTLKKSVQEGKVSMETLNTACRRILEAKYKLGLFDNPYKYCDPKRPARDIFTKAHRDAARRIAAESFVLLKNDSPDGNPNGNPLLPFNPKGNIAVIGPLANSRSNMPGTWSVAAVLDRCPSLVEGLKEMTAGKANIMYAKGSNLISDASYEERATMFGRSLNRDNRTDQQLLDEALNVARRSDIIIAALGESSEMSGESSSRTDLNIPDVQQNLLKELLKTGKPVVLVLFTGRPLTLNWEQEHVPAILNVWFGGSEAAYAIGDALFGYVNPGGKLTMTFPKNVGQIPLYYAQKNTGRPLKDGKWFEKFRSNYLDVDNDPLYPFGYGLSYTTFSYSDIDLSHSSMDMNGSLTAAVEVTNTGTWPGSEVVQLYIRDVVGSSTRPVKELKGFQKIFLEPGEMKIVRFKIAPEMLRYYNYDLQLVAEPGDFEVMIGTNSRDVKTAKFTLN

Source

organism	Bacteroides ovatus ATCC 8483
ncbi_taxonomy_id	411476
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	beta-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1223

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6. Citations (1)

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length_a	68.833 Å
length_b	74.965 Å
length_c	87.009 Å
angle_alpha	72.86 °
angle_beta	67.76 °
angle_gamma	64.84 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.950 Å
resolution_low	38.670 Å
r_factor	0.2036
r_work	0.2017
r_free	0.2366

fit	/app/data/saxs_computation/ur/9urg/9urg.fit
pddf	/app/data/pr_computation/ur/9urg/9urg.pr.out
profile	/app/data/saxs_computation/ur/9urg/9urg.dat

Crystal structure of beta-glucosidase from Bacteroides ovatus bound to beta-D-Glucose

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