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9ug5

Crystal structure of HA3 from Clostridium botulinum type B with alpha2,3-sialyllactose

Method: X-RAY DIFFRACTION D_max: 183.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ug5
deposition_date	2025-04-11
last_revision	2025-11-05
title	Crystal structure of HA3 from Clostridium botulinum type B with alpha2,3-sialyllactose
keywords	Clostridium botulinum, BoNT, hemagglutinin, HA, HA3, type B, Okra, 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	51.86 Å
rg_electron	52.12 Å
i0	530633000.00
molecular_weight	193130.0 kDa
excluded_volume	242360 Å³
envelope_volume	378920 Å³
shell_volume	64083 Å³
envelope_diameter	181.2 Å
shell_rg	51.23 Å
envelope_rg	50.90 Å
shape_rg	52.13 Å
total_rg	52.05 Å
total_atoms	13662
n_residues	1718
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	183.0 Å
rg_real	52.06 Å
rg_real_error	2.07 Å
i0_real	5.3060e+08
i0_real_error	1.0020e+07
rg_reciprocal	51.68 Å
i0_reciprocal	530300000.0000
total_estimate	0.8514
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	61.0 Å
skewness	0.427
kurtosis	-0.313
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	19310000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.777

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	13678

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-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
formula_weight	633.6 kDa
src_method	man
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	16

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6. Citations (1)

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length_a	81.974 Å
length_b	144.091 Å
length_c	158.032 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	3.000 Å
resolution_low	44.320 Å
r_factor	0.2277
r_work	0.2238
r_free	0.3026

fit	/app/data/saxs_computation/ug/9ug5/9ug5.fit
pddf	/app/data/pr_computation/ug/9ug5/9ug5.pr.out
profile	/app/data/saxs_computation/ug/9ug5/9ug5.dat

Crystal structure of HA3 from Clostridium botulinum type B with alpha2,3-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