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10qf

Crystal Structure of Treponema denticola Sialidase (TDE_0471)

Method: X-RAY DIFFRACTION D_max: 88.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10qf
deposition_date	2026-02-01
last_revision	2026-02-25
title	Crystal Structure of Treponema denticola Sialidase (TDE_0471)
keywords	sialidase, neuraminidase, virulence factor, 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	25.00 Å
rg_electron	23.99 Å
i0	61004400.00
molecular_weight	58293.0 kDa
excluded_volume	71186 Å³
envelope_volume	82119 Å³
shell_volume	28900 Å³
envelope_diameter	90.9 Å
shell_rg	30.99 Å
envelope_rg	24.43 Å
shape_rg	23.86 Å
total_rg	25.06 Å
total_atoms	4024
n_residues	500
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	88.1 Å
rg_real	25.04 Å
rg_real_error	0.76 Å
i0_real	6.1000e+07
i0_real_error	8.8700e+05
rg_reciprocal	25.03 Å
i0_reciprocal	61000000.0000
total_estimate	0.8346
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.8 Å
skewness	0.496
kurtosis	0.096
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	12530000.0000
n_real_points	64
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	exo-alpha-sialidase
formula_weight	58788.7 kDa
ec_number	3.2.1.18
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4746

MRGSHHHHHHGSANKKDGGNQQGGLNPPSPGTPTFTVTFDVQGRGKTPAALTVPKDSLLTAAQTPPLEFSGWEFGGWYKDAFKTHEWNNASDTVTENTTLYARWTHTYPPAVQDLWQSKTDRPEDFYRIPALAVTKDGTLLAVTDLRYKNNSDLGNNHRIDLLIKRSEDNGKAWSEAVNITKTLPTDQTGYGDAAIVADRESDDVLILCVHGNVTYQAGNASNHLKVIQFVSHDGGKTFPEKKDISNTIFGFNHSWFSLFFGSGRIMQSRYIKAGSHYRIYSALLSKRFIHSNDHHDNAVVYSDDFGSTWHVLGDASTSPIPDGNEAKVEELPDGSVILSSRNGTANGRLINIFTYSDPDTGAGSWSSKQFLNLGSGSGTNGEILILKARKTDTKDPVYLAFQSLPDGPGRSKVTIHWRELTNNTITAHDFVSAATWNSHSYVVQTGDSAYSTMDVQRDGGIGFLYERNTRGLEYDIAYKNLPIDVITNGAYEAIFLGTGSVQCPYTDLEGKPVDPSVKEYYKNEKLHWKE

Source

organism	Treponema denticola
ncbi_taxonomy_id	158
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	CADMIUM ION
formula_weight	112.4 kDa
src_method	syn
entity_count	14

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	282.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CITRIC ACID
formula_weight	192.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	14

Entity 7 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	479

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6. Citations (1)

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length_a	129.794 Å
length_b	65.479 Å
length_c	92.042 Å
angle_alpha	90.00 °
angle_beta	106.78 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.627 Å
resolution_low	45.709 Å
r_factor	—
r_work	0.1638
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