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9x8f

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

Method: X-RAY DIFFRACTION D_max: 96.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x8f
deposition_date	2025-10-19
last_revision	2026-04-29
title	Crystal structure of the N-terminal of an alpha-amylase family glycosyl hydrolase from Vibrio parahaemolyticus
keywords	alpha-amylase family 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	28.50 Å
rg_electron	27.76 Å
i0	86420500.00
molecular_weight	71251.0 kDa
excluded_volume	88013 Å³
envelope_volume	104720 Å³
shell_volume	32126 Å³
envelope_diameter	100.2 Å
shell_rg	34.45 Å
envelope_rg	28.27 Å
shape_rg	27.77 Å
total_rg	28.32 Å
total_atoms	5017
n_residues	633
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	96.6 Å
rg_real	28.64 Å
rg_real_error	0.72 Å
i0_real	8.6420e+07
i0_real_error	1.1850e+06
rg_reciprocal	28.60 Å
i0_reciprocal	86420000.0000
total_estimate	0.8615
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.1 Å
skewness	0.497
kurtosis	-0.212
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	15370000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.922

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Alpha-amylase
formula_weight	71284.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5291

DTGSHVASPDWQDQIIYFLMIDRFNDGDSALNDQGQNEFDPTSDKKFSGGDLVGVSDKLSYIEDLGATSIWITPPVANQWWDTEQNYGGYHGYWARDFQKVDEHFGDMESYQALAREVHARNMFLIQDIVTNHVGNFFTYDDPYSYDPSLPCQGFRLIKNALPAGQELPYPLNMNECKTDGTGSYHWTPTITDHNDPVQEKTWQLSDLDDLNTSDPEVRAYLKESYRKWIREVGVDGFRIDTVKFVEHDFWNDFLHADDGVMTQAVDTGRDNFLTFGEVFETSTPYHTEGEEKMLTYIGESGSPKQLTSVLNFPLQATMTRVFASGQPTDYLRFRLEKMMEMFPNPYIMPNFIDNHDMPRFLSQGSVNDMKQALITMMSVPGIPVIYQGTEQAMSSARDAMFAGGYREDGNYVDSFDQNSEMYLFIQELAKLRTENRVMTRGEMKVIGSDKAGAGVFAFTRTLDNDEVLVVMNTSNSPMLMNQLDVEQVGGTVFQQQIMSNWAEAPEQLIADENGHVTLELPAKSAVIYSKTSSNQSVNTPDLNIQLAQDWEGKTITGDIVIAGSANANEKLNLVVDGNLETAQTITVGADGQFSVTLSTRHFAIGEQQHRFAIYSTEKKAGIEDVNFVSNLS

Source

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

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	274

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6. Citations (1)

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length_a	118.770 Å
length_b	118.770 Å
length_c	107.930 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	1.960 Å
resolution_low	24.000 Å
r_factor	0.2009
r_work	0.1986
r_free	0.2463

fit	/app/data/saxs_computation/x8/9x8f/9x8f.fit
pddf	/app/data/pr_computation/x8/9x8f/9x8f.pr.out
profile	/app/data/saxs_computation/x8/9x8f/9x8f.dat

Crystal structure of the N-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