SAXSdb — 10qf

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

exo-alpha-sialidase

Treponema denticola

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 25–543	Not recorded	CD CADMIUM ION × 14 NA SODIUM ION × 2 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 14 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；296 K；25 mM Citric acid, 75 mM Bis-tris propane, pH 7.4, 20 mM Cadmium chloride, 25% PEG400, seeded	Resolution 1.63 Å R-free 0.187

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 10QF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10QG Crystal Structure of Treponema denticola Sialidase (TDE_0471) bound to Neu5Ac2en (DANA) Deposited 2026-02-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–543（519 aa）	Not recorded	DAN 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID × 2 EDO 1,2-ETHANEDIOL × 5 PEG DI(HYDROXYETHYL)ETHER × 2 CD CADMIUM ION × 23	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；296 K；100 mM HEPES, pH 7.8, 20 mM Cadmium chloride, 25% PEG400, soak in mother liquor with 25 mM DANA for 20 min	Resolution 1.55 Å R-free 0.153
10QH Crystal Structure of Treponema denticola Sialidase (TDE_0471) Bound to Neu5Ac (NANA) Deposited 2026-02-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–543（519 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 17 SLB N-acetyl-beta-neuraminic acid × 1 EDO 1,2-ETHANEDIOL × 9 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；296 K；100 mM Tris, pH 8.2, 20 mM Cadmium chloride, 25% PEG400, soak in mother liquor with 15 mM Neu5Ac	Resolution 1.56 Å R-free 0.158
10QI Crystal Structure of Treponema denticola Sialidase (TDE_0471) D165A mutant bound to 3'-sialyllactose (only Neu5Ac visible) Deposited 2026-02-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–543（519 aa）	Mutation：D165A	SIA N-acetyl-alpha-neuraminic acid × 1 GOL GLYCEROL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 CD CADMIUM ION × 6 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；296 K；100 mM Bis-tris, pH 6.5, 20 mM Cadmium chliride, 23% PEG400, 5 mM 3'-sialyllactose	Resolution 1.81 Å R-free 0.190

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q73QH2_TREDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–531； UniProt 25–543

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	10qf
Deposition date deposition_date	2026-02-01
最后修订 last_revision	2026-02-25
Structure title title	Crystal Structure of Treponema denticola Sialidase (TDE_0471)
Keywords keywords	sialidase, neuraminidase, virulence factor, 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	25.00 Å
Radius of gyration Rg (electron density) rg_electron	23.99 Å
Forward intensity I(0) i0	61004400.00
Molecular weight molecular_weight	58293.0 kDa
Excluded volume excluded_volume	71186 Å³
Envelope volume envelope_volume	82119 Å³
Hydration-shell volume shell_volume	28900 Å³
Envelope diameter envelope_diameter	90.9 Å
Shell Rg shell_rg	30.99 Å
Envelope Rg envelope_rg	24.43 Å
Shape Rg shape_rg	23.86 Å
Total Rg total_rg	25.06 Å
Total atoms total_atoms	4024
Residues n_residues	500
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	88.1 Å
Rg (real space) rg_real	25.04 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	6.1000e+07
I(0) uncertainty (real space) i0_real_error	8.8700e+05
Rg (reciprocal space) rg_reciprocal	25.03 Å
I(0) (reciprocal space) i0_reciprocal	61000000.0000
Solution quality estimate total_estimate	0.8346
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.8 Å
Skewness Skewness skewness	0.496
Kurtosis Kurtosis kurtosis	0.096
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12530000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.651; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.946

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	exo-alpha-sialidase
Molecular weight formula_weight	58788.7 kDa
EC 编号 ec_number	3.2.1.18
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4746

MRGSHHHHHHGSANKKDGGNQQGGLNPPSPGTPTFTVTFDVQGRGKTPAALTVPKDSLLTAAQTPPLEFSGWEFGGWYKDAFKTHEWNNASDTVTENTTLYARWTHTYPPAVQDLWQSKTDRPEDFYRIPALAVTKDGTLLAVTDLRYKNNSDLGNNHRIDLLIKRSEDNGKAWSEAVNITKTLPTDQTGYGDAAIVADRESDDVLILCVHGNVTYQAGNASNHLKVIQFVSHDGGKTFPEKKDISNTIFGFNHSWFSLFFGSGRIMQSRYIKAGSHYRIYSALLSKRFIHSNDHHDNAVVYSDDFGSTWHVLGDASTSPIPDGNEAKVEELPDGSVILSSRNGTANGRLINIFTYSDPDTGAGSWSSKQFLNLGSGSGTNGEILILKARKTDTKDPVYLAFQSLPDGPGRSKVTIHWRELTNNTITAHDFVSAATWNSHSYVVQTGDSAYSTMDVQRDGGIGFLYERNTRGLEYDIAYKNLPIDVITNGAYEAIFLGTGSVQCPYTDLEGKPVDPSVKEYYKNEKLHWKE

来源 Source

来源生物 organism	Treponema denticola
NCBI Class编号 ncbi_taxonomy_id	158
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 7 Entity 7 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	479

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8. Citations (1)

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Unit-cell length a length_a	129.794 Å
Unit-cell length b length_b	65.479 Å
Unit-cell length c length_c	92.042 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.627 Å
Low-resolution limit resolution_low	45.709 Å
R factor r_factor	—
R_work r_work	0.1638
R_free r_free	0.1869

fit	/app/data/saxs_computation/0q/10qf/10qf.fit
pddf	/app/data/pr_computation/0q/10qf/10qf.pr.out
profile	/app/data/saxs_computation/0q/10qf/10qf.dat

Crystal Structure of Treponema denticola Sialidase (TDE_0471)

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

exo-alpha-sialidase

State in the Current Structure

Other States of the Same Protein in the Database

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