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9s8f

Amuc1755_S1_16 in complex with D-Galactose

Method: X-RAY DIFFRACTION D_max: 73.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s8f
deposition_date	2025-08-05
last_revision	2026-06-03
title	Amuc1755_S1_16 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	23.44 Å
rg_electron	22.20 Å
i0	61159000.00
molecular_weight	60043.0 kDa
excluded_volume	74674 Å³
envelope_volume	84583 Å³
shell_volume	30214 Å³
envelope_diameter	74.9 Å
shell_rg	30.74 Å
envelope_rg	22.67 Å
shape_rg	22.19 Å
total_rg	23.13 Å
total_atoms	4227
n_residues	532
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	73.2 Å
rg_real	23.28 Å
rg_real_error	0.34 Å
i0_real	6.1160e+07
i0_real_error	7.5870e+05
rg_reciprocal	23.32 Å
i0_reciprocal	61160000.0000
total_estimate	0.8966
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.4 Å
skewness	0.159
kurtosis	-0.401
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	20110000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Sulfatase
formula_weight	59893.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4387

AAEPKRPNIILFLVDDMGWQDTSLPFWREEDGTPKPTFLNKRYRTPNMEALGKQGMVFTNAYAQPICSPSRCSLMSGMNSARHRVTNWTLLRDQTTDAGHQALKAPADWSVNGIQPAGTRASGTTHLPLTEEKIQYRMEKPFTQVLGLPALLKKQGYTTIHCGKAHFGSKNTPGANPRLFGFDYNIAGTEIGGPADYRGSRKYGTGNFHVRGLDENNYYENDTFLTEALTQEALKRLDAIRKNPREADKPFYLYMSHYAIHAPFDMRGYDKRFAEEYSNPNDGHKWSDNEKRYSALIQGMDKSLGDIREYLKKNNLDKNTVIIFMADNGGLAISGRMGNKESNYPLSFGKGSNREGGIREPMIVYWPGVTKAESVCTTPVIIEDFFPTILEIAGAKKIQAPQVVDGKSFVALLKGGSMNPNRSLLFHTPNVWGEGNGNNSLYSPSTAMRQGDWKLIYWHPDQKFELFNLKEDISEEHNLAEQQPERVKVMARTMTTLLKERKAQMPTYKKNNPAGAREGAPVPWPDQAAARL

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	1

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	116

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6. Citations (1)

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length_a	143.080 Å
length_b	143.080 Å
length_c	50.410 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 64
int_tables_number	172
crystal_system	—

resolution	2.100 Å
resolution_low	71.540 Å
r_factor	—
r_work	0.1662
r_free	0.2072

fit	/app/data/saxs_computation/s8/9s8f/9s8f.fit
pddf	/app/data/pr_computation/s8/9s8f/9s8f.pr.out
profile	/app/data/saxs_computation/s8/9s8f/9s8f.dat

Amuc1755_S1_16 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