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- PDB-9ug5: Crystal structure of HA3 from Clostridium botulinum type B with a... -

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Basic information

Entry
Database: PDB / ID: 9ug5
TitleCrystal structure of HA3 from Clostridium botulinum type B with alpha2,3-sialyllactose
ComponentsHA3
KeywordsTOXIN / Clostridium botulinum / BoNT / hemagglutinin / HA / HA3 / type B / Okra / Sialyllactose
Function / homologyHemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium enterotoxin / Clostridium enterotoxin / extracellular region / 3'-sialyl-alpha-lactose / HA3
Function and homology information
Biological speciesClostridium botulinum B1 str. Okra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAmatsu, S. / Kitadokoro, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Gut mucin fucosylation dictates the entry of botulinum toxin complexes
Authors: Amatsu, S. / Matsumura, T. / Morimoto, C. / Keisham, S. / Goto, Y. / Kohda, T. / Hirabayashi, J. / Kitadokoro, K. / Katayama, T. / Kiyono, H. / Tateno, H. / Zuka, M. / Fujinaga, Y.
History
DepositionApr 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HA3
B: HA3
C: HA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,6555
Polymers215,3873
Non-polymers1,2672
Water28816
1
A: HA3

B: HA3
hetero molecules

C: HA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,6555
Polymers215,3873
Non-polymers1,2672
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area11870 Å2
ΔGint-36 kcal/mol
Surface area69020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.974, 144.091, 158.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HA3


Mass: 71795.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum B1 str. Okra (bacteria)
Gene: ha3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q33CP8
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7 / Details: 14% PEG 3350 and 0.1 M BisTris HCl pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 34819 / % possible obs: 90.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.105 / Χ2: 1.041 / Net I/σ(I): 7.1 / Num. measured all: 125357
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
3-3.113.50.5013.133391.05488.2
3.11-3.233.60.36633451.04388
3.23-3.383.60.26833541.04688.3
3.38-3.563.60.20833341.06387.8
3.56-3.783.60.15233361.05787.6
3.78-4.073.60.12133401.04487.3
4.07-4.483.50.09334441.05189.7
4.48-5.133.50.08336280.96493.5
5.13-6.463.70.07337921.05897.4
6.46-503.70.04639071.03795.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→44.32 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.826 / SU B: 26.189 / SU ML: 0.461 / Cross valid method: THROUGHOUT / ESU R Free: 0.62 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30258 1749 5.1 %RANDOM
Rwork0.22379 ---
obs0.2277 32677 90.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.961 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 3→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13576 0 86 16 13678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01213932
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612784
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.79918956
X-RAY DIFFRACTIONr_angle_other_deg0.4791.74329410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.97451697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.373547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.679102241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.22166
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023276
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7536.296849
X-RAY DIFFRACTIONr_mcbond_other4.7536.296849
X-RAY DIFFRACTIONr_mcangle_it7.611.2748523
X-RAY DIFFRACTIONr_mcangle_other7.59911.2748524
X-RAY DIFFRACTIONr_scbond_it4.5416.4737083
X-RAY DIFFRACTIONr_scbond_other4.5416.4737082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.37611.84210434
X-RAY DIFFRACTIONr_long_range_B_refined10.8485.6514566
X-RAY DIFFRACTIONr_long_range_B_other10.8485.6514566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 134 -
Rwork0.322 2309 -
obs--87.66 %

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