SAXSdb — 9sf6

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1. Structure Basics

entry_id	9sf6
deposition_date	2025-08-19
last_revision	2026-06-03
title	Amuc0953 N-terminal domain
keywords	Carbohydrate binding module, mucin, Akkermansia muciniphila, Sulfation, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	39.37 Å
rg_electron	39.28 Å
i0	168818000.00
molecular_weight	99069.0 kDa
excluded_volume	121380 Å³
envelope_volume	170360 Å³
shell_volume	37761 Å³
envelope_diameter	119.1 Å
shell_rg	42.46 Å
envelope_rg	39.18 Å
shape_rg	39.33 Å
total_rg	39.32 Å
total_atoms	6955
n_residues	936
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	120.4 Å
rg_real	39.44 Å
rg_real_error	0.92 Å
i0_real	1.6880e+08
i0_real_error	2.9630e+06
rg_reciprocal	39.40 Å
i0_reciprocal	168800000.0000
total_estimate	0.8263
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	45.2 Å
skewness	0.193
kurtosis	-0.889
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	13000000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.897; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Sulfatase
formula_weight	48901.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	7220

ADVEYVWRGVDYQWGSLSNWSVGGIAASSAPGAAASAYEHWMVTNGTDSAGRTDVGGLGAGGRYLKGVRIEGLNSQPEGKIPLFIKNTNKDVYLRVEEGGITVENAGEGGYSADFGVAQLRVAADQEWHVAEGRSLYVGHDDDAPSGGLYSLTSEGDVPRRVTVTGGGAVRIGEGMLLNNISGLIGFVLNAGKGIPTLDLADRGMGNTVTVEDAARLEGMSLYQGALVTRENASVTFSGTEAKASGQWNIGADTELALENSTLDLTEAGVDGNVILSGSSGITGDKGTLRQTLLDDARVTYTDRNVKAGEIRSVGSNVTITLNNSSMHFDGEIPEVDLVVQGSCALGGSGAFSGTITYAPGGTLTVDGDISLPSSSLTLGRLHVATLDGVPQNSAVRPETPAQQAREYVVLFDSSFEDLISEWPGRHTLGVQFRPDMGAPVTVKELPEGAVSWNYDAASGWLTLQTDV

Source

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

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	15

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	265

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6. Citations (1)

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length_a	100.440 Å
length_b	59.150 Å
length_c	111.120 Å
angle_alpha	90.00 °
angle_beta	95.11 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	55.340 Å
r_factor	—
r_work	0.1921
r_free	0.2321

fit	/app/data/saxs_computation/sf/9sf6/9sf6.fit
pddf	/app/data/pr_computation/sf/9sf6/9sf6.pr.out
profile	/app/data/saxs_computation/sf/9sf6/9sf6.dat

Amuc0953 N-terminal domain

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