SAXSdb — 9x1i

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1. Structure Basics

entry_id	9x1i
deposition_date	2025-10-02
last_revision	2026-03-18
title	Structure of endo-beta-N-acetylglucosaminidase HS
keywords	endo-beta-N-acetylglucosaminidase, 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	46.54 Å
rg_electron	46.49 Å
i0	706424000.00
molecular_weight	213890.0 kDa
excluded_volume	264690 Å³
envelope_volume	345040 Å³
shell_volume	63387 Å³
envelope_diameter	154.3 Å
shell_rg	49.01 Å
envelope_rg	45.91 Å
shape_rg	46.45 Å
total_rg	46.72 Å
total_atoms	15086
n_residues	1944
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	154.6 Å
rg_real	46.84 Å
rg_real_error	1.62 Å
i0_real	7.0640e+08
i0_real_error	1.3600e+07
rg_reciprocal	46.55 Å
i0_reciprocal	706200000.0000
total_estimate	0.8274
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.9 Å
skewness	0.399
kurtosis	-0.701
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	95780000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.718; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.656

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Endo-beta-N-acetylglucosaminidase HS
formula_weight	108932.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	17463

MSTASTQVFDLSKLGDQTLLEHFAQLLDNGKKYPTDADLTAWGIKDEVEFIRSHVRKRAIESRADRLLQDTYENRNLFMNIPGGAGKNLGGYPSKTFANDNFSMWNYTNLFGAWNYGLFQAPGSWADAAHRNGTSIFAGIKFFDHTTGGAANSWASFIMTRNTDGSFRYTHPIINCMRFLGFDGINYNWESTNKYQDADNIAFHKELYKIAKSEGFNDFKIMYYTTSSSLTSYSSRYMWGQDKDNRICEVMLNYDNSDFSWNMGSSVKEAERTMGSADGLYAGVWIVSMDRRWNSLNNQDAKRCGICLWGEHAESRFWSYNTGGDAMSRMSNYQEYLERAFSGGNRNPLYRPEISNRGNNVEAQGTTPPLARFAGLASWIPERTAISGNLPFATHFNTGNGERYNYKGKKTAGSWYNMSSQDVVPTYRWMVVKPETEVASTDVQPSFTNEDAYTGGAALRLKGVNNATATDVVLFKTNLTPSKGKVVAKVAIKTGKEGNNDSKLSLIVRVNGAWKAYALGNTENANWTEKKVELNDITAGQKIERIGLRVKDSDADYNVLVGKLELNDDVTATPANVKDLTVQVKEETKNSLSVKAVWGIDKDPGQNPTVYNDEANIDHFEILYKNGENGKVSEVGRTSQWATLVPNIQFTSVDDKPFIGVRSVSTDLKTYSKTQWIAVPRAQQSELPEAQEEGYGTVELDNAAAGADVAKRIRYVKKFQTEGGSKNIDYTAEGPAGNETNYVDATSQELEVAQGATVKVKIQGYEATQIKDQSNDDLRYCMGKAWMDFNGDKQFNPENLSENPNEGECVVFFGQVRKGVPAQVQQLNEYTFKVPEDAKPGQSRLRLVFCDAWFQGGLTPTGKFNKGFAIDFKVTITGSNAARGAKADTHDKGVADEPELLEGGSTNIISANVGGASQLTVVGGKVVFENVERAWVFSTDGQTVKSLVNPKSFNTNELPAGVYLVKMQNNNVIRTQKITIK

Source

organism	human oral metagenome
ncbi_taxonomy_id	447426
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2377

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6. Citations (1)

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length_a	71.927 Å
length_b	135.567 Å
length_c	238.865 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.810 Å
resolution_low	39.050 Å
r_factor	0.1981
r_work	0.1959
r_free	0.2421

fit	/app/data/saxs_computation/x1/9x1i/9x1i.fit
pddf	/app/data/pr_computation/x1/9x1i/9x1i.pr.out
profile	/app/data/saxs_computation/x1/9x1i/9x1i.dat

Structure of endo-beta-N-acetylglucosaminidase HS

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