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- PDB-3ah1: HA1 subcomponent of botulinum type C progenitor toxin complexed w... -

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Basic information

Entry
Database: PDB / ID: 3ah1
TitleHA1 subcomponent of botulinum type C progenitor toxin complexed with N-acetylneuramic acid
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
N-acetyl-beta-neuraminic acid / Main hemagglutinin component type C / Main hemagglutinin component type C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: 2EHI
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)69,0865
Polymers68,1582
Non-polymers9283
Water4,864270
1
A: Main hemagglutinin component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6973
Polymers34,0791
Non-polymers6192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Main hemagglutinin component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3882
Polymers34,0791
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-15 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.320, 61.722, 82.397
Angle α, β, γ (deg.)90.00, 104.28, 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-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 50.81 %
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: Jan 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 32592 / Num. obs: 32591 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 5 / Num. unique all: 3038 / % possible all: 88.7

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Processing

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

1qxm


Resolution: 2.2→46.05 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1876143.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3249 10 %RANDOM
Rwork0.205 ---
obs0.205 32591 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.6112 Å2 / ksol: 0.377516 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.23 Å20 Å2-2.19 Å2
2--2.68 Å20 Å2
3---1.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4763 0 63 270 5096
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 508 10.3 %
Rwork0.228 4439 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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