← Back to search

10qh

Crystal Structure of Treponema denticola Sialidase (TDE_0471) Bound to Neu5Ac (NANA)

Method: X-RAY DIFFRACTION D_max: 87.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	10qh
deposition_date	2026-02-01
last_revision	2026-02-25
title	Crystal Structure of Treponema denticola Sialidase (TDE_0471) Bound to Neu5Ac (NANA)
keywords	sialidase, neuraminidase, virulence factor, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	24.66 Å
rg_electron	23.71 Å
i0	61984100.00
molecular_weight	58294.0 kDa
excluded_volume	70847 Å³
envelope_volume	80920 Å³
shell_volume	28720 Å³
envelope_diameter	95.0 Å
shell_rg	30.79 Å
envelope_rg	24.14 Å
shape_rg	23.61 Å
total_rg	24.64 Å
total_atoms	4006
n_residues	499
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

▼

3. P(r) Analysis (GNOM)

dmax	87.6 Å
rg_real	24.68 Å
rg_real_error	0.73 Å
i0_real	6.1980e+07
i0_real_error	9.4400e+05
rg_reciprocal	24.67 Å
i0_reciprocal	61980000.0000
total_estimate	0.5661
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	30.6 Å
skewness	0.481
kurtosis	0.104
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	14930000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.621; Stabil: 0.997; Sysdev: 0.184; Positv: 1.000; Valcen: 0.950; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	exo-alpha-sialidase
formula_weight	58804.7 kDa
ec_number	3.2.1.18
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4784

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	17

Entity 3 non-polymer

description	N-acetyl-beta-neuraminic acid
formula_weight	309.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	9

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	498

▶

6. Citations (1)

▶

length_a	129.734 Å
length_b	65.371 Å
length_c	92.021 Å
angle_alpha	90.00 °
angle_beta	106.19 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.560 Å
resolution_low	57.950 Å
r_factor	0.1427
r_work	0.1418
r_free	0.1585

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