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9urf

Crystal structure of beta-glucosidase from Bacteroides ovatus

Method: X-RAY DIFFRACTION D_max: 110.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9urf
deposition_date	2025-04-29
last_revision	2026-05-20
title	Crystal structure of beta-glucosidase from Bacteroides ovatus
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	34.92 Å
rg_electron	34.17 Å
i0	414431000.00
molecular_weight	164300.0 kDa
excluded_volume	205160 Å³
envelope_volume	243910 Å³
shell_volume	57090 Å³
envelope_diameter	114.8 Å
shell_rg	42.70 Å
envelope_rg	34.36 Å
shape_rg	34.14 Å
total_rg	34.83 Å
total_atoms	11536
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	110.0 Å
rg_real	34.78 Å
rg_real_error	0.58 Å
i0_real	4.1440e+08
i0_real_error	5.7760e+06
rg_reciprocal	34.87 Å
i0_reciprocal	414500000.0000
total_estimate	0.8979
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.5 Å
skewness	0.202
kurtosis	-0.489
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0001
highest_alpha	101000000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.905

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	13465

MASWSHPQFEKGSSHHHHHHSSGSGGGGGENLYFQGSNRDKINYNNMIYKKLSLSVLLFAAGFLTASAQKSPQDMDRFIDVLMNKMTLEEKIGQLNLPVTGEITTGQAKSSDIAAKIKKGEVGGLFNLKGVEKIREVQKQAVEDSRLGIPLLFGMDVIHGYETMFPIPLGLSCTWDMTAIEESARIAAVEASADGISWTFSPMVDISRDPRWGRVSEGSGEDPFLGAMIAEAMVRGYQGKNMERNDEIMACVKHFALYGAGEAGRDYNTVDMSRQRMFNDYMLPYEAAVEAGVGSVMASFNEVDGIPATANKWLMTDILRGQWGFNGFVVTDYTGISEMIDHGIGDLQTVSARAINAGVDMDMVSEGFVGTLKKSVQEGKVSMETLNTACRRILEAKYKLGLFDNPYKYCDPKRPARDIFTKAHRDAARRIAAESFVLLKNDSPDGNPNGNPLLPFNPKGNIAVIGPLANSRSNMPGTWSVAAVLDRCPSLVEGLKEMTAGKANIMYAKGSNLISDASYEERATMFGRSLNRDNRTDQQLLDEALNVARRSDIIIAALGESSEMSGESSSRTDLNIPDVQQNLLKELLKTGKPVVLVLFTGRPLTLNWEQEHVPAILNVWFGGSEAAYAIGDALFGYVNPGGKLTMTFPKNVGQIPLYYAQKNTGRPLKDGKWFEKFRSNYLDVDNDPLYPFGYGLSYTTFSYSDIDLSHSSMDMNGSLTAAVEVTNTGTWPGSEVVQLYIRDVVGSSTRPVKELKGFQKIFLEPGEMKIVRFKIAPEMLRYYNYDLQLVAEPGDFEVMIGTNSRDVKTAKFTLN

Source

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

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1739

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6. Citations (1)

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length_a	68.653 Å
length_b	74.665 Å
length_c	86.751 Å
angle_alpha	72.86 °
angle_beta	67.70 °
angle_gamma	64.78 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	1.400 Å
resolution_low	40.960 Å
r_factor	0.1712
r_work	0.1701
r_free	0.1914

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

Crystal structure of beta-glucosidase from Bacteroides ovatus

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