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10qg

Crystal Structure of Treponema denticola Sialidase (TDE_0471) bound to Neu5Ac2en (DANA)

Method: X-RAY DIFFRACTION D_max: 89.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10qg
deposition_date	2026-02-01
last_revision	2026-02-25
title	Crystal Structure of Treponema denticola Sialidase (TDE_0471) bound to Neu5Ac2en (DANA)
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	24.83 Å
rg_electron	23.84 Å
i0	65621700.00
molecular_weight	58991.0 kDa
excluded_volume	71092 Å³
envelope_volume	81210 Å³
shell_volume	28731 Å³
envelope_diameter	93.1 Å
shell_rg	30.82 Å
envelope_rg	24.25 Å
shape_rg	23.72 Å
total_rg	24.86 Å
total_atoms	4015
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	89.7 Å
rg_real	24.86 Å
rg_real_error	0.75 Å
i0_real	6.5620e+07
i0_real_error	1.0300e+06
rg_reciprocal	24.85 Å
i0_reciprocal	65620000.0000
total_estimate	0.8252
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.3 Å
skewness	0.488
kurtosis	0.133
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	12850000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.600; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	4914

MRGSHHHHHHGSANKKDGGNQQGGLNPPSPGTPTFTVTFDVQGRGKTPAALTVPKDSLLTAAQTPPLEFSGWEFGGWYKDAFKTHEWNNASDTVTENTTLYARWTHTYPPAVQDLWQSKTDRPEDFYRIPALAVTKDGTLLAVTDLRYKNNSDLGNNHRIDLLIKRSEDNGKAWSEAVNITKTLPTDQTGYGDAAIVADRESDDVLILCVHGNVTYQAGNASNHLKVIQFVSHDGGKTFPEKKDISNTIFGFNHSWFSLFFGSGRIMQSRYIKAGSHYRIYSALLSKRFIHSNDHHDNAVVYSDDFGSTWHVLGDASTSPIPDGNEAKVEELPDGSVILSSRNGTANGRLINIFTYSDPDTGAGSWSSKQFLNLGSGSGTNGEILILKARKTDTKDPVYLAFQSLPDGPGRSKVTIHWRELTNNTITAHDFVSAATWNSHSYVVQTGDSAYSTMDVQRDGGIGFLYERNTRGLEYDIAYKNLPIDVITNGAYEAIFLGTGSVQCPYTDLEGKPVDPSVKEYYKNEKLHWKE

Source

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

Entity 2 non-polymer

description	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
formula_weight	291.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	nat
entity_count	5

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CADMIUM ION
formula_weight	112.4 kDa
src_method	syn
entity_count	23

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	555

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6. Citations (1)

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length_a	129.811 Å
length_b	65.547 Å
length_c	91.679 Å
angle_alpha	90.00 °
angle_beta	106.15 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.549 Å
resolution_low	59.314 Å
r_factor	—
r_work	0.1378
r_free	0.1530

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