SAXSdb — 9s8x

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1. Structure Basics

entry_id	9s8x
deposition_date	2025-08-05
last_revision	2026-06-03
title	Amuc0953_S1_20 in complex with D-Galactose
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	60.28 Å
rg_electron	60.01 Å
i0	1132750000.00
molecular_weight	271130.0 kDa
excluded_volume	334170 Å³
envelope_volume	542100 Å³
shell_volume	75939 Å³
envelope_diameter	207.8 Å
shell_rg	61.93 Å
envelope_rg	57.76 Å
shape_rg	59.99 Å
total_rg	60.11 Å
total_atoms	19074
n_residues	2526
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	202.0 Å
rg_real	60.21 Å
rg_real_error	2.87 Å
i0_real	1.1330e+09
i0_real_error	2.3870e+07
rg_reciprocal	60.30 Å
i0_reciprocal	1133000000.0000
total_estimate	0.8473
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	101.0 Å
skewness	0.066
kurtosis	-0.713
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	31000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.773

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Sulfatase
formula_weight	135282.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	19074

ADVEYVWRGVDYQWGSLSNWSVGGIAASSAPGAAASAYEHWMVNAGTDSAGRTDVGGLGAGGRYLKGVRIEGLNSQPEGKIPLFIKNTNKDVYLRVEEGGITVENAGEGGYSADFGVAQLRVAADQEWHVAEGRSLYVGHDDDAPSGGLCSLTSEGDVPRRVTVTGGGAVRIGEGMLLNNISGLIGFVLNAGKGIPTLDLADRGMGNTVTVEDAARLEGMSLYQGALVTRENASVTFSGTEAKASGQWNIGADTELALENSTLDLTEAGVDGNVILSGSSGITGDKGTLRQTLLDDARVTYTDRNVKAGEIRSVGSNVTITLNNSSMHFDGEIPEVDLVVQGSCALGGSGAFSGTITYAPGGTLTVDGDISLPSSSLTLGRLHVATLDGVPQNSAVRPETPAQQAREYVVLFDSSFEDLISEWPGRHTLGVQFRPDMGAPVTVKELPEGAVSWNYDAASGWLTLQTDVAEKPDMPAHVSGARPNIIFVLVDDMGWGDMSVNWTQQDKNGRQVTRRNEFKTPTLDTMAAEGMQLRRHYSAAPVCAPARASLLLGVHQGHSRVVRNNTFDYPIENSHTLGTLLKSAGYHTAAIGKWGVGGGGQSGKALTAAPHMRGFDYFYGIIKHLAGHYHYLTAGSQDIYEYNDQAAAPAWESVSAKVPGTAYDTDLFGARAKQWIVDHHEKTPSRPFFLYLAFPAPHGCLSAPACAYPAGLGRDGGLQWEKKDGYEACNTAADGWSGVEGDFSPDTYIYPEHEVFGRTESRHATMIRRVDDVLKDMIQLLKDLGIDDNTMIVFTSDNGPHNEPGSGNYGNGAQDPAYFMSYGMMDGIKRDCWEGGMRVPAVVRWPGVVPSGISLNASQFQDWMATFADVAGVPVPSRCDGVSLLPTLAGVPERQKTGVIYAEYAYSGSTPNYSDFLQQHRGRGRQQQQIIFVDGFKGIRMGNAAPATDFEIYDTEKDPQEAANLAASRPDLQEKMKAQALRSRRSSPIASTSFDTSYIAPVSAPAGLREGRLRWRAWNRSFDWVPDFRQLEEGPCSTGATDVSDVLSVKAGLSGQKGVELTGYLRVPVTGEYQFYLQTDSNEGSRAFVHLHDMQLIDADYAYTPGTQAASNAREGVSGDVQPNAVQTVKLTAGLHPIRIGYVGKAASSSLSLQWEGPETSGREPIPASAFSYEYVNPFNLEKTEETVGCAASGTGLTVQTHLPWTVSCDQPWVTVSPVSGSGTSVLDIAVEANGLQTEREAVVTVVCGGEQRTFTLRQEAAP

Source

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

Entity 2 non-polymer

description	beta-D-galactopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	IODIDE ION
formula_weight	126.9 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	187.280 Å
length_b	187.280 Å
length_c	221.770 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 41
int_tables_number	80
crystal_system	—

resolution	2.900 Å
resolution_low	78.476 Å
r_factor	—
r_work	0.2118
r_free	0.2566

fit	/app/data/saxs_computation/s8/9s8x/9s8x.fit
pddf	/app/data/pr_computation/s8/9s8x/9s8x.pr.out
profile	/app/data/saxs_computation/s8/9s8x/9s8x.dat

Amuc0953_S1_20 in complex with D-Galactose

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