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- PDB-3aj5: HA1 (HA33) subcomponent of botulinum type C progenitor toxin comp... -

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Basic information

Entry
Database: PDB / ID: 3aj5
TitleHA1 (HA33) subcomponent of botulinum type C progenitor toxin complexed with N-acetylgalactosamine, bound at site II
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
2-acetamido-2-deoxy-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: 1.8 Å
AuthorsNakamura, T. / Tonozuka, T. / Sato, R. / Oguma, K. / Nishikawa, A.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2011
Title: Molecular diversity of the two sugar-binding sites of the beta-trefoil lectin HA33/C (HA1) from Clostridium botulinum type C neurotoxin
Authors: Nakamura, T. / Tonozuka, T. / Ito, S. / Takeda, Y. / Sato, R. / Matsuo, I. / Ito, Y. / Oguma, K. / Nishikawa, A.
#1: 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.
History
DepositionMay 24, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,0014
Polymers67,5592
Non-polymers4422
Water13,133729
1
A: Main hemagglutinin component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0012
Polymers33,7791
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Main hemagglutinin component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0012
Polymers33,7791
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-10 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.424, 62.187, 82.436
Angle α, β, γ (deg.)90.00, 104.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Main hemagglutinin component / HA 33 kDa subunit / HA1


Mass: 33779.488 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-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% ethanol, 1.7M sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 62088 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6068 / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0099refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AH2

3ah2


Resolution: 1.8→31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: THROUGHOUT / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20209 3148 5.1 %RANDOM
Rwork0.16488 ---
obs0.1668 58932 98.45 %-
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: 18.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 30 729 5479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224926
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9166728
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2285588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07425.776277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61215857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.451520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023798
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_it0.6641.52864
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27324690
X-RAY DIFFRACTIONr_scbond_it1.93632062
X-RAY DIFFRACTIONr_scangle_it3.1344.52026
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 225 -
Rwork0.223 4207 -
obs--95.5 %

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