SAXSdb — 9x1i

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1. Protein Identity and Related Structures Protein Identity & Related Structures

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric	Entity 1：Endo-beta-N-acetylglucosaminidase HS × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	GOL GLYCEROL × 3 SO4 SULFATE ION × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；2.0M Ammonium sulfate, 0.1M Bis-Tris-HCl buffer	Resolution 1.81 Å R-free 0.242
2	Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric	Entity 1：Endo-beta-N-acetylglucosaminidase HS × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；2.0M Ammonium sulfate, 0.1M Bis-Tris-HCl buffer	Resolution 1.81 Å R-free 0.242

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9x1i
Deposition date deposition_date	2025-10-02
最后修订 last_revision	2026-03-18
Structure title title	Structure of endo-beta-N-acetylglucosaminidase HS
Keywords keywords	endo-beta-N-acetylglucosaminidase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	46.54 Å
Radius of gyration Rg (electron density) rg_electron	46.49 Å
Forward intensity I(0) i0	706424000.00
Molecular weight molecular_weight	213890.0 kDa
Excluded volume excluded_volume	264690 Å³
Envelope volume envelope_volume	345040 Å³
Hydration-shell volume shell_volume	63387 Å³
Envelope diameter envelope_diameter	154.3 Å
Shell Rg shell_rg	49.01 Å
Envelope Rg envelope_rg	45.91 Å
Shape Rg shape_rg	46.45 Å
Total Rg total_rg	46.72 Å
Total atoms total_atoms	15086
Residues n_residues	1944
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	154.6 Å
Rg (real space) rg_real	46.84 Å
Rg uncertainty (real space) rg_real_error	1.62 Å
I(0) (real space) i0_real	7.0640e+08
I(0) uncertainty (real space) i0_real_error	1.3600e+07
Rg (reciprocal space) rg_reciprocal	46.55 Å
I(0) (reciprocal space) i0_reciprocal	706200000.0000
Solution quality estimate total_estimate	0.8274
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.9 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.701
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	95780000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Endo-beta-N-acetylglucosaminidase HS
Molecular weight formula_weight	108932.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	17463

MSTASTQVFDLSKLGDQTLLEHFAQLLDNGKKYPTDADLTAWGIKDEVEFIRSHVRKRAIESRADRLLQDTYENRNLFMNIPGGAGKNLGGYPSKTFANDNFSMWNYTNLFGAWNYGLFQAPGSWADAAHRNGTSIFAGIKFFDHTTGGAANSWASFIMTRNTDGSFRYTHPIINCMRFLGFDGINYNWESTNKYQDADNIAFHKELYKIAKSEGFNDFKIMYYTTSSSLTSYSSRYMWGQDKDNRICEVMLNYDNSDFSWNMGSSVKEAERTMGSADGLYAGVWIVSMDRRWNSLNNQDAKRCGICLWGEHAESRFWSYNTGGDAMSRMSNYQEYLERAFSGGNRNPLYRPEISNRGNNVEAQGTTPPLARFAGLASWIPERTAISGNLPFATHFNTGNGERYNYKGKKTAGSWYNMSSQDVVPTYRWMVVKPETEVASTDVQPSFTNEDAYTGGAALRLKGVNNATATDVVLFKTNLTPSKGKVVAKVAIKTGKEGNNDSKLSLIVRVNGAWKAYALGNTENANWTEKKVELNDITAGQKIERIGLRVKDSDADYNVLVGKLELNDDVTATPANVKDLTVQVKEETKNSLSVKAVWGIDKDPGQNPTVYNDEANIDHFEILYKNGENGKVSEVGRTSQWATLVPNIQFTSVDDKPFIGVRSVSTDLKTYSKTQWIAVPRAQQSELPEAQEEGYGTVELDNAAAGADVAKRIRYVKKFQTEGGSKNIDYTAEGPAGNETNYVDATSQELEVAQGATVKVKIQGYEATQIKDQSNDDLRYCMGKAWMDFNGDKQFNPENLSENPNEGECVVFFGQVRKGVPAQVQQLNEYTFKVPEDAKPGQSRLRLVFCDAWFQGGLTPTGKFNKGFAIDFKVTITGSNAARGAKADTHDKGVADEPELLEGGSTNIISANVGGASQLTVVGGKVVFENVERAWVFSTDGQTVKSLVNPKSFNTNELPAGVYLVKMQNNNVIRTQKITIK

来源 Source

来源生物 organism	human oral metagenome
NCBI Class编号 ncbi_taxonomy_id	447426
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2377

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8. Citations (1)

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Unit-cell length a length_a	71.927 Å
Unit-cell length b length_b	135.567 Å
Unit-cell length c length_c	238.865 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	39.050 Å
R factor r_factor	0.1981
R_work r_work	0.1959
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Assembly Composition of the Current Entry

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction