SAXSdb — 9s8a

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1. Structure Basics

entry_id	9s8a
deposition_date	2025-08-05
last_revision	2026-06-03
title	Amuc0451_S1_20
keywords	Carbohydrate sulfatase, mucin, Akkermansia muciniphila, Sulfation, 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	35.65 Å
rg_electron	35.63 Å
i0	359703000.00
molecular_weight	152090.0 kDa
excluded_volume	189540 Å³
envelope_volume	228690 Å³
shell_volume	52928 Å³
envelope_diameter	128.8 Å
shell_rg	42.14 Å
envelope_rg	36.00 Å
shape_rg	35.60 Å
total_rg	36.11 Å
total_atoms	10731
n_residues	1363
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	119.5 Å
rg_real	35.76 Å
rg_real_error	0.93 Å
i0_real	3.5970e+08
i0_real_error	6.2760e+06
rg_reciprocal	35.69 Å
i0_reciprocal	359700000.0000
total_estimate	0.8679
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.0 Å
skewness	0.489
kurtosis	-0.179
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	125500000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.863

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Sulfatase
formula_weight	75251.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	11917

SKPNVIFILVDDMGWGDLDSNWSQQKLNGRTVERKNEFKTPALSALAREGIQLRRHYSAAPVCAPARASLLLGVHQGNSRVVRNNRFDQPIEDSHTLGTVMRDAGYDTAAIGKWGVGGGGQSHVPMTAGPHQRGFNYFYGILDHLAGHFHYPSESRDVFEYNGYASNPEWKNIKDQVPQTAYSTDLFAARAKQWIVDQRKSARKTGKPFFLYLAFPAPHGNLVVPGVPYPSGGGLKGGLQWVKKEGTESVNTAFDAKAEKNKDTYIHPDNSRFPNDVAKRHSTMIRRVDDAVADLIRLLKDLKIDDNTMIVFTSDNGPHNEGGSDSRHWHGAQNPQFFKSYGMMDGIKRDCWEGGMRVPTLVRWPARIPKGQISLHPGQFHDWLATLADVAGVPVPARSDGVSLLPTLTGHADQQKPGIVYAEYNFAGKTPEYKDFLGEHKGAQRGQQQIVFVDGLKGLRMGVKDADKDFMIFDTLNDPQESKDLASSKPELQARMKAAALSNRRASLPSKTVFDSALVPAVDVKGTVSPGLRWALYEGDFPWVPDFRQWKKPASAHGVTPSPSVKMNGSDKRGVELTGYVKIPEDGAYTFYLTTDENKGSKAFVRLHGMELIDADKTYEPGAEVSSDLGDRKNPVYLKAGLHPIRIGYVGNSGTASKLVLKWEGPGLPKQEIPASAFSHGK

Source

organism	Akkermansia muciniphila ATCC BAA-835
ncbi_taxonomy_id	349741
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	27

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	948

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6. Citations (1)

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length_a	113.660 Å
length_b	59.900 Å
length_c	123.720 Å
angle_alpha	90.00 °
angle_beta	115.75 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.600 Å
resolution_low	51.754 Å
r_factor	—
r_work	0.1556
r_free	0.1915

fit	/app/data/saxs_computation/s8/9s8a/9s8a.fit
pddf	/app/data/pr_computation/s8/9s8a/9s8a.pr.out
profile	/app/data/saxs_computation/s8/9s8a/9s8a.dat

Amuc0451_S1_20

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