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9s8y

Amuc1074_S1_11 in complex with N-acetyl D-glucosamine

Method: X-RAY DIFFRACTION D_max: 74.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s8y
deposition_date	2025-08-05
last_revision	2026-06-03
title	Amuc1074_S1_11 in complex with N-acetyl D-glucosamine
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	23.70 Å
rg_electron	22.77 Å
i0	60401200.00
molecular_weight	60589.0 kDa
excluded_volume	75676 Å³
envelope_volume	85857 Å³
shell_volume	30135 Å³
envelope_diameter	77.1 Å
shell_rg	31.14 Å
envelope_rg	23.25 Å
shape_rg	22.75 Å
total_rg	23.76 Å
total_atoms	4264
n_residues	522
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	74.1 Å
rg_real	23.56 Å
rg_real_error	0.42 Å
i0_real	6.0400e+07
i0_real_error	8.6700e+05
rg_reciprocal	23.60 Å
i0_reciprocal	60400000.0000
total_estimate	0.8172
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	28.9 Å
skewness	0.207
kurtosis	-0.409
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	17190000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Sulfatase
formula_weight	59956.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4909

KKPNILFIITDDHAYQTLGTGNNDSPVALPNFNKLGRQGMVFDRSYCANSLCGPSRACILTGRHSHMNGFVFNGQRPLDGSQPTYPKMLQKAGYQTGLFGKWHLESDPTGFDTWEIFPGQGSYYNPDFISLKPDGKRQTKRFPGYATDVVTDKSIQWLENRDKNKPFLLVVGHKAPHRAWCPALRHLGKVDTSSMTPPANFHDDYANRPEFLKKNQQTVANHMAIYSDLKVLKDQVPEEMRKSIVSPGYGWDLGELNRMTPEEKKTWTDYYAKRTKSLVDGMKSGKLKDPKAFAEWKWHAYMEDYLGCLLSVDDSIGRLMEYLDKEGIAKDTLVIYCGDQGFYMGEHGMYDKRWIFEESLRMPLIMRWPGKIPAGIRNNTMVQNIDYAPTIVSAAGADTPENMNTFQGVSLLPTAFTGKTPDNWRDAIYYCFYENPGEHNAPRHDGIRTDRYTLSYIWTSGEWMLFDMKKDPMQMKNVIDDPAYKTTVEQLKKRYHELRKTYKVPENSPGGKGTPIPKFDASW

Source

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

Entity 2 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-acetamido-2-deoxy-alpha-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
formula_weight	208.3 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	437

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6. Citations (1)

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length_a	130.010 Å
length_b	130.010 Å
length_c	86.270 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 41
int_tables_number	80
crystal_system	—

resolution	1.380 Å
resolution_low	41.147 Å
r_factor	—
r_work	0.1673
r_free	0.1841

fit	/app/data/saxs_computation/s8/9s8y/9s8y.fit
pddf	/app/data/pr_computation/s8/9s8y/9s8y.pr.out
profile	/app/data/saxs_computation/s8/9s8y/9s8y.dat