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9x81

Crystal structure of the C-terminal of an alpha-amylase family glycosyl hydrolase from Vibrio parahaemolyticus

Method: X-RAY DIFFRACTION D_max: 85.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x81
deposition_date	2025-10-18
last_revision	2026-04-29
title	Crystal structure of the C-terminal of an alpha-amylase family glycosyl hydrolase from Vibrio parahaemolyticus
keywords	alpha-amylase, glycosyl 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	24.20 Å
rg_electron	23.75 Å
i0	20522600.00
molecular_weight	33690.0 kDa
excluded_volume	41720 Å³
envelope_volume	49665 Å³
shell_volume	19358 Å³
envelope_diameter	86.9 Å
shell_rg	28.40 Å
envelope_rg	24.12 Å
shape_rg	23.74 Å
total_rg	24.36 Å
total_atoms	2380
n_residues	311
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	85.9 Å
rg_real	24.53 Å
rg_real_error	0.80 Å
i0_real	2.0520e+07
i0_real_error	3.1130e+05
rg_reciprocal	24.46 Å
i0_reciprocal	20520000.0000
total_estimate	0.7935
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.8 Å
skewness	0.657
kurtosis	-0.103
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	3953000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.604; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.604; Smooth: 0.897

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Alpha-amylase
formula_weight	33613.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2568

PDLNIQLAQDWEGKTITGDIVIAGSANANEKLNLVVDGNLETAQTITVGADGQFSVTLSTRHFAIGEQQHRFAIYSTEKKAGIEDVNFVSNLSWSNTPDDTIDDAGDAQDGVGGPNGNYSLPTDPTFDKDNSQLAINKAEVFTVGSNVRLTFTMDKITDTWLPPNGFDHVGFTIFIDLPEEAATNLSELPKINASMPSGTWSRNAVVFGWQSSIYNTKGANATTWGEAVTPAPTVTVDKANNTISMDFASDALGRPDSLDGIRFYVTTWDLDGLSATYRPLEQDKGPWNFSGGASDESKIWDDLPIITLSE

Source

organism	Vibrio parahaemolyticus
ncbi_taxonomy_id	670
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	nat
entity_count	1

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	188

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6. Citations (1)

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length_a	47.700 Å
length_b	67.830 Å
length_c	86.210 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.420 Å
resolution_low	22.000 Å
r_factor	0.1780
r_work	0.1764
r_free	0.2114

fit	/app/data/saxs_computation/x8/9x81/9x81.fit
pddf	/app/data/pr_computation/x8/9x81/9x81.pr.out
profile	/app/data/saxs_computation/x8/9x81/9x81.dat

Crystal structure of the C-terminal of an alpha-amylase family glycosyl hydrolase from Vibrio parahaemolyticus

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