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9ug6

Crystal structure of HA3 from Clostridium botulinum type B with alpha2,6-sialyllactose

Method: X-RAY DIFFRACTION D_max: 152.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ug6
deposition_date	2025-04-11
last_revision	2025-11-05
title	Crystal structure of HA3 from Clostridium botulinum type B with alpha2,6-sialyllactose
keywords	Clostridium botulinum, botulinum toxin, BoNT, hemagglutinin, HA, sialyllactose, TOXIN; TOXIN
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	47.19 Å
rg_electron	46.55 Å
i0	560983000.00
molecular_weight	198080.0 kDa
excluded_volume	248540 Å³
envelope_volume	367300 Å³
shell_volume	65670 Å³
envelope_diameter	154.5 Å
shell_rg	51.77 Å
envelope_rg	44.74 Å
shape_rg	46.53 Å
total_rg	46.83 Å
total_atoms	27559
n_residues	1751
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	152.2 Å
rg_real	46.99 Å
rg_real_error	1.17 Å
i0_real	5.6100e+08
i0_real_error	1.0210e+07
rg_reciprocal	47.19 Å
i0_reciprocal	561100000.0000
total_estimate	0.8918
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.6 Å
skewness	0.101
kurtosis	-0.546
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	31600000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.881

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	HA3
formula_weight	71795.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	27749

MASWSHPQFEKGALEVLFQGPGYQYSDTIDLADGNYVVSRGDGWILSRQNQILGGSVISNGSTGIVGDLRVNDNAIPYYYPTPSFNEEYIKNNIQTVFANFTEANQIPIGFEFSKTAPSNKNLYMYLQYTYIRYEIIKVLQHEIIERAVLYVPSLGYVKSIEFNPGEKINKDFYFLTNDKCILNEQFLYKKILETTKNIPTNNIFNSKVSSTQRVLPYSNGLYVINKGDGYIRTNDKDLIGTLLIEAGSSGSIIQPRLRNTTRPLFTTSNDAKFSQQYTEERLKDAFNVQLFNTSTSLFKFVEEAPSNKNICIKAYNTYEKYELIDYQNGSIVNKAEYYLPSLGYCEVTNAPSPESEVVKTQVAEDGFIQNGPEEEIVVGVIDPSENIQEINTAISDNYTYNIPGIVNNNPFYILFTVNTTGIYKINAQNNLPSLKIYEAIGSGNRNFQSGNLCDDDIKAINYITGFDSPNAKSYLVVLLNKDKNYYIRVPQTSSNIENQIKFKREEGDLRNLMNSSVNIIDNLNSTGAHYYTRQSPDVHDYISYEFTIPGNFNNKDTSNIRLYTSYNQGIGTLFRVTETIDGYNLINIQQNLNLLNSTKSIRLLNGAIYILKVEVTELNNYNIKLHIDITN

Source

organism	Clostridium botulinum B1 str. Okra
ncbi_taxonomy_id	498213
host_organism	Escherichia coli

Entity 2 branched

description	N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-glucopyranose
formula_weight	471.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	190

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6. Citations (1)

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length_a	84.251 Å
length_b	145.697 Å
length_c	159.708 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.230 Å
resolution_low	42.110 Å
r_factor	0.2321
r_work	0.2292
r_free	0.2873

fit	/app/data/saxs_computation/ug/9ug6/9ug6.fit
pddf	/app/data/pr_computation/ug/9ug6/9ug6.pr.out
profile	/app/data/saxs_computation/ug/9ug6/9ug6.dat

Crystal structure of HA3 from Clostridium botulinum type B with alpha2,6-sialyllactose

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction