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9qqo

Crystal structure of a beta-glycosidase from Prevotella sp.

Method: X-RAY DIFFRACTION D_max: 181.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qqo
deposition_date	2025-04-01
title	Crystal structure of a beta-glycosidase from Prevotella sp.
keywords	glycoside hydrolase, 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	59.87 Å
rg_electron	59.33 Å
i0	5250970000.00
molecular_weight	610530.0 kDa
excluded_volume	761120 Å³
envelope_volume	1039400 Å³
shell_volume	142400 Å³
envelope_diameter	184.1 Å
shell_rg	64.34 Å
envelope_rg	57.44 Å
shape_rg	59.31 Å
total_rg	59.52 Å
total_atoms	43293
n_residues	5336
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	181.0 Å
rg_real	59.52 Å
rg_real_error	1.40 Å
i0_real	5.2510e+09
i0_real_error	1.0390e+08
rg_reciprocal	60.14 Å
i0_reciprocal	5256000000.0000
total_estimate	0.8349
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	69.6 Å
skewness	0.076
kurtosis	-0.596
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	161100000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Beta-glycosidase
formula_weight	51484.7 kDa
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	46238

MHHHHHHSFKKDFIWGTATASYQVEGAAFEDGKGLNIWDAFSHIDGKVFDNHNGDTACDCYHRLDGDLDLMKSLGVNSYRFSVSWSRIIPDGAGEVNPKGLDFYSRLIDGLISRGIKPCMTLYHWDLPYALHLKGGWLNDDMPDIFAAYAKLIKEQFGGRVHDFITFNEPQVFVGCGYLEGKHAPGYRLAKPELMRIGHNVLKAHGKAVLELRKGEPCRIGISSASQPAIPVSAEDTAAARENYFQSDHPAFPFSDAYWLDPMINGRYPDWVYECKEPNAPVITDEDLKLISQPIDFIGMNIYNGRYIHGGEVRKFKTGMTRTSIGWPVTPEALYWGPYFYYERYKKPIVITENGMACHDRVSSDGKVHDPNRIEYLREYLQNFRKAAEDGVDADGYYIWSFMDNFEWSDGYKERFGIVYNDYETQQRTVKDSALWYKDVISSNGENLR

Source

organism	Prevotella
ncbi_taxonomy_id	838
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	12

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2945

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6. Citations (1)

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length_a	134.182 Å
length_b	139.490 Å
length_c	172.660 Å
angle_alpha	90.00 °
angle_beta	99.84 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.500 Å
resolution_low	114.280 Å
r_factor	0.1698
r_work	0.1691
r_free	0.1823

fit	/app/data/saxs_computation/qq/9qqo/9qqo.fit
pddf	/app/data/pr_computation/qq/9qqo/9qqo.pr.out
profile	/app/data/saxs_computation/qq/9qqo/9qqo.dat

Crystal structure of a beta-glycosidase from Prevotella sp.

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