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9x3m

Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidase in complex with xylose.

Method: X-RAY DIFFRACTION D_max: 177.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x3m
deposition_date	2025-10-09
last_revision	2026-01-07
title	Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidase in complex with xylose.
keywords	beta-xylosidase, Xylose, 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	52.86 Å
rg_electron	52.67 Å
i0	2079560000.00
molecular_weight	389290.0 kDa
excluded_volume	488600 Å³
envelope_volume	656820 Å³
shell_volume	101800 Å³
envelope_diameter	184.7 Å
shell_rg	57.53 Å
envelope_rg	51.59 Å
shape_rg	52.66 Å
total_rg	52.85 Å
total_atoms	27492
n_residues	3456
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	177.1 Å
rg_real	52.86 Å
rg_real_error	1.56 Å
i0_real	2.0800e+09
i0_real_error	3.9900e+07
rg_reciprocal	52.83 Å
i0_reciprocal	2079000000.0000
total_estimate	0.8725
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.0 Å
skewness	0.338
kurtosis	-0.446
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	133800000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.810

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Xylan 1,4-beta-xylosidase
formula_weight	48510.5 kDa
ec_number	3.2.1.37
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	27742

QNPIIQTMYTADPAPMVYNNRLYVYTTHDEDQSTWFNMNDWKVYSTNDMVNWTDHGTILKYSDFAWAKGDAWAAQCVEKNGKFYLYVPVVSKVNNKGAIGVAVGDSPLGPFYDVLGKPLVQSEWGDIDPTVFIDDDGQAHMYWGNPKLKYVKLNEDMISYSGDIIEVPMTEESFGKRDGNPERPTKYEEGPWLYKRKDLYYLFWPGGPLPEFIGYSTSKSAKGPWKYGGIVMPAEGKSFTNHPGVIDFRGKTYFFYHNGALPGGSGFTRSVCVQELNFNKDGTIPQMKMTEGITKGIAALNPYQLTQAETISWSEHVKAFQNDKVGVFVRALQNGAYTSVKNVDFGDIGASAFSARVGTTHNGGVTMEIRMGSQEGPIAGTVKVPLTGGDDRWEIINVKLDRKITGIQDVYFVFKGKASSNIMYFDYWKFSK

Source

organism	Pseudopedobacter saltans DSM 12145
ncbi_taxonomy_id	762903
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	16

Entity 3 non-polymer

description	D-xylose
formula_weight	150.1 kDa
src_method	syn
entity_count	8

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	244

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6. Citations (1)

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length_a	73.585 Å
length_b	89.435 Å
length_c	138.443 Å
angle_alpha	102.82 °
angle_beta	94.02 °
angle_gamma	97.88 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.800 Å
resolution_low	47.841 Å
r_factor	—
r_work	0.2183
r_free	0.2728

fit	/app/data/saxs_computation/x3/9x3m/9x3m.fit
pddf	/app/data/pr_computation/x3/9x3m/9x3m.pr.out
profile	/app/data/saxs_computation/x3/9x3m/9x3m.dat

Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidase in complex with xylose.

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