Improved thermostability of a GH10 xylanase based on its X-ray crystal structure

Method: X-RAY DIFFRACTION D_max: 85.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9upa
deposition_date	2025-04-28
last_revision	2025-06-11
title	Improved thermostability of a GH10 xylanase based on its X-ray crystal structure
keywords	glycosidase, crystal, thermostability, HYDROLASE, CARBOHYDRATE; CARBOHYDRATE
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	28.14 Å
rg_electron	27.22 Å
i0	100699000.00
molecular_weight	78837.0 kDa
excluded_volume	98763 Å³
envelope_volume	118450 Å³
shell_volume	35745 Å³
envelope_diameter	87.2 Å
shell_rg	35.16 Å
envelope_rg	26.64 Å
shape_rg	27.16 Å
total_rg	28.18 Å
total_atoms	5548
n_residues	706
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	85.1 Å
rg_real	27.99 Å
rg_real_error	0.44 Å
i0_real	1.0070e+08
i0_real_error	1.3820e+06
rg_reciprocal	28.04 Å
i0_reciprocal	100700000.0000
total_estimate	0.9135
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	33.4 Å
skewness	0.155
kurtosis	-0.625
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	24800000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.962

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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	53.350 Å
length_b	69.300 Å
length_c	91.080 Å
angle_alpha	90.00 °
angle_beta	91.91 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.600 Å
resolution_low	46.694 Å
r_factor	—
r_work	0.2420
r_free	0.2947

description	Beta-xylanase
formula_weight	39489.5 kDa
ec_number	3.2.1.8
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	5629

Improved thermostability of a GH10 xylanase 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	Massilia sp. RBM26
ncbi_taxonomy_id	1756047
host_organism	Escherichia coli

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	81

fit	/app/data/saxs_computation/up/9upa/9upa.fit
pddf	/app/data/pr_computation/up/9upa/9upa.pr.out
profile	/app/data/saxs_computation/up/9upa/9upa.dat