The X-ray Crystallographic Structure of oligo-1,6-glucosidase from Paenibacillus sp. STB16

Method: X-RAY DIFFRACTION D_max: 114.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u7v
deposition_date	2025-03-25
last_revision	2025-05-07
title	The X-ray Crystallographic Structure of oligo-1,6-glucosidase from Paenibacillus sp. STB16
keywords	oligo-1, 6-glucosidase, Mesophilic amylase, Isomaltooligosaccharide debranching enzyme, 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	34.83 Å
rg_electron	34.29 Å
i0	258164000.00
molecular_weight	126460.0 kDa
excluded_volume	156460 Å³
envelope_volume	191000 Å³
shell_volume	46394 Å³
envelope_diameter	115.6 Å
shell_rg	40.83 Å
envelope_rg	34.04 Å
shape_rg	34.27 Å
total_rg	34.77 Å
total_atoms	8927
n_residues	1090
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	114.0 Å
rg_real	34.88 Å
rg_real_error	1.08 Å
i0_real	2.5820e+08
i0_real_error	4.8350e+06
rg_reciprocal	34.85 Å
i0_reciprocal	258200000.0000
total_estimate	0.8864
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.5 Å
skewness	0.373
kurtosis	-0.499
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	54810000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.910

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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	154.570 Å
length_b	154.570 Å
length_c	115.174 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 4 21 2
int_tables_number	90
crystal_system	—

resolution	3.240 Å
resolution_low	31.440 Å
r_factor	0.3071
r_work	0.3049
r_free	0.3497

description	oligo-1,6-glucosidase
formula_weight	67123.8 kDa
ec_number	3.2.1.10
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	8992

The X-ray Crystallographic Structure of oligo-1,6-glucosidase from Paenibacillus sp. STB16

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	Paenibacillus
ncbi_taxonomy_id	44249
host_organism	Bacillus subtilis

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	65

fit	/app/data/saxs_computation/u7/9u7v/9u7v.fit
pddf	/app/data/pr_computation/u7/9u7v/9u7v.pr.out
profile	/app/data/saxs_computation/u7/9u7v/9u7v.dat