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- PDB-9ug6: Crystal structure of HA3 from Clostridium botulinum type B with a... -

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Basic information

Entry
Database: PDB / ID: 9ug6
TitleCrystal structure of HA3 from Clostridium botulinum type B with alpha2,6-sialyllactose
ComponentsHA3
KeywordsTOXIN / Clostridium botulinum / botulinum toxin / BoNT / hemagglutinin / HA / sialyllactose
Function / homologyHemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium enterotoxin / Clostridium enterotoxin / extracellular region / N-acetyl-alpha-neuraminic acid / HA3
Function and homology information
Biological speciesClostridium botulinum B1 str. Okra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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)216,1685
Polymers215,3873
Non-polymers7812
Water3,423190
1
A: HA3

C: HA3
hetero molecules

B: HA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,1685
Polymers215,3873
Non-polymers7812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area11800 Å2
ΔGint-35 kcal/mol
Surface area70280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.251, 145.697, 159.708
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-(2-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DNeup5Aca2-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+2)][a-D-9-deoxy-Neup5Ac]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
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: 2.23→50 Å / Num. obs: 95640 / % possible obs: 98.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.064 / Χ2: 1.025 / Net I/σ(I): 13.8 / Num. measured all: 410454
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.23-2.3140.24891781.019196
2.31-2.44.10.19594620.991198.3
2.4-2.514.10.15994850.991198.9
2.51-2.644.20.12395560.987199
2.64-2.814.20.09295771.006199.4
2.81-3.034.30.06895871.033199.3
3.03-3.334.40.04896311.05199.4
3.33-3.814.50.04296661.114199.3
3.81-4.84.60.07396800.973198.8
4.8-504.50.04598181.078196.5

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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: 2.23→42.11 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.028 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28726 4570 5 %RANDOM
Rwork0.22924 ---
obs0.23213 86718 94.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.866 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.23→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13958 0 52 190 14200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01214290
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613193
X-RAY DIFFRACTIONr_angle_refined_deg1.821.80319448
X-RAY DIFFRACTIONr_angle_other_deg0.6131.74930335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.45751742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.067554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89102354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.22197
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023399
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 339 -
Rwork0.268 6280 -
obs--94.53 %

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