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- PDB-3ah4: HA1 subcomponent of botulinum type C progenitor toxin complexed w... -

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Basic information

Entry
Database: PDB / ID: 3ah4
TitleHA1 subcomponent of botulinum type C progenitor toxin complexed with galactose
ComponentsMain hemagglutinin component
KeywordsTOXIN / beta trefoil / hemagglutinin
Function / homology
Function and homology information


carbohydrate binding / extracellular region
Similarity search - Function
Ricin-type beta-trefoil lectin domain-like / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Main hemagglutinin component type C / Main hemagglutinin component type C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsNakamura, T. / Tonozuka, T. / Ide, A. / Yuzawa, T. / Oguma, K. / Nishikawa, A.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Sugar-binding sites of the HA1 subcomponent of Clostridium botulinum type C progenitor toxin
Authors: Nakamura, T. / Tonozuka, T. / Ide, A. / Yuzawa, T. / Oguma, K. / Nishikawa, A.
#1: Journal: Biochim.Biophys.Acta / Year: 2007
Title: Binding properties of Clostridium botulinum type C progenitor toxin to mucins
Authors: Nakamura, T. / Takada, N. / Tonozuka, T. / Sakano, Y. / Oguma, K. / Nishikawa, A.
#2: Journal: Biochim.Biophys.Acta / Year: 2006
Title: Cell internalization and traffic pathway of Clostridium botulinum type C neurotoxin in HT-29 cells
Authors: Uotsu, N. / Nishikawa, A. / Watanabe, T. / Ohyama, T. / Tonozuka, T. / Sakano, Y. / Oguma, K.
History
DepositionApr 13, 2010Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 28, 2010ID: 2EHN
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Main hemagglutinin component
B: Main hemagglutinin component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5184
Polymers68,1582
Non-polymers3602
Water13,691760
1
A: Main hemagglutinin component


Theoretical massNumber of molelcules
Total (without water)34,0791
Polymers34,0791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Main hemagglutinin component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4393
Polymers34,0791
Non-polymers3602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-10 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.921, 62.176, 82.270
Angle α, β, γ (deg.)90.00, 104.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Main hemagglutinin component / HA1 subcomponent of botulinum type C progenitor toxin / hemagglutinin component HA1 / HA 33 kDa subunit / HA1


Mass: 34078.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: type C / Plasmid: pMAL-2X FLAG-HA1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P46084, UniProt: P0DPR0*PLUS
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% ethanol, 1.7M sodium chloride, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 63127 / Num. obs: 63127 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 31.3
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 6.8 / Num. unique all: 5877 / % possible all: 91.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.5.0099refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QXM

1qxm


Resolution: 1.78→39.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20089 6387 10.1 %RANDOM
Rwork0.16412 ---
obs0.16783 56829 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.485 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.78→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4735 0 24 760 5519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9166674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2245578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70725.912274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26615846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3731518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023756
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6151.52856
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17524670
X-RAY DIFFRACTIONr_scbond_it1.80132035
X-RAY DIFFRACTIONr_scangle_it2.9154.51998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.779→1.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 451 -
Rwork0.196 3737 -
obs--88.45 %

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