Improved thermostability of a GH3 glycosidase based on its X-ray crystal structure

Method: X-RAY DIFFRACTION D_max: 87.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ul7
deposition_date	2025-04-19
last_revision	2025-06-11
title	Improved thermostability of a GH3 glycosidase based on its X-ray crystal structure
keywords	glycosidase, crystal, thermostability, 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	26.43 Å
rg_electron	25.45 Å
i0	73606600.00
molecular_weight	65627.0 kDa
excluded_volume	81385 Å³
envelope_volume	96227 Å³
shell_volume	31562 Å³
envelope_diameter	91.4 Å
shell_rg	32.82 Å
envelope_rg	25.59 Å
shape_rg	25.42 Å
total_rg	26.24 Å
total_atoms	4631
n_residues	601
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	87.3 Å
rg_real	26.42 Å
rg_real_error	0.48 Å
i0_real	7.3610e+07
i0_real_error	1.0040e+06
rg_reciprocal	26.42 Å
i0_reciprocal	73610000.0000
total_estimate	0.8833
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.0 Å
skewness	0.398
kurtosis	-0.190
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	18930000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	112.866 Å
length_b	104.617 Å
length_c	69.156 Å
angle_alpha	90.00 °
angle_beta	91.91 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.200 Å
resolution_low	34.559 Å
r_factor	0.1917
r_work	0.1895
r_free	0.2361

description	beta-glucosidase
formula_weight	67835.2 kDa
ec_number	3.2.1.21
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	4877

Improved thermostability of a GH3 glycosidase based on its X-ray crystal structure

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Clavibacter michiganensis
ncbi_taxonomy_id	28447
host_organism	Escherichia coli

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	246

fit	/app/data/saxs_computation/ul/9ul7/9ul7.fit
pddf	/app/data/pr_computation/ul/9ul7/9ul7.pr.out
profile	/app/data/saxs_computation/ul/9ul7/9ul7.dat