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- PDB-2zs6: HA3 subcomponent of botulinum type C progenitor toxin -

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Basic information

Entry
Database: PDB / ID: 2zs6
TitleHA3 subcomponent of botulinum type C progenitor toxin
Components(Hemagglutinin components HA3) x 2
KeywordsTOXIN / LECTIN / HEMAGGLUTININ / BOTULINUM TOXIN
Function / homology
Function and homology information


symbiont-mediated migration across host transepithelium / extracellular region
Similarity search - Function
Jelly Rolls - #1080 / Jelly Rolls - #1090 / Proaerolysin; Chain A, domain 3 - #20 / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium enterotoxin / Beta Complex / Jelly Rolls ...Jelly Rolls - #1080 / Jelly Rolls - #1090 / Proaerolysin; Chain A, domain 3 - #20 / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium enterotoxin / Beta Complex / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hemagglutinin components HA-70 type C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNakamura, T. / Tonozuka, T. / Kotani, M. / Oguma, K. / Nishikawa, A.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of the HA3 Subcomponent of Clostridium botulinum Type C Progenitor Toxin
Authors: Nakamura, T. / Kotani, M. / Tonozuka, T. / Ide, A. / 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.
#2: 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.
History
DepositionSep 2, 2008Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 16, 2008ID: 2Z5A
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin components HA3
B: Hemagglutinin components HA3


Theoretical massNumber of molelcules
Total (without water)71,2892
Polymers71,2892
Non-polymers00
Water4,107228
1
A: Hemagglutinin components HA3
B: Hemagglutinin components HA3

A: Hemagglutinin components HA3
B: Hemagglutinin components HA3

A: Hemagglutinin components HA3
B: Hemagglutinin components HA3


Theoretical massNumber of molelcules
Total (without water)213,8676
Polymers213,8676
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area24850 Å2
ΔGint-100 kcal/mol
Surface area71270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.397, 176.397, 80.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Hemagglutinin components HA3 / HA-22-23


Mass: 23955.641 Da / Num. of mol.: 1 / Fragment: HA3a
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: type C / Plasmid: pMAL-cRI / Production host: Escherichia coli (E. coli) / References: UniProt: P46085
#2: Protein Hemagglutinin components HA3 / HA-53


Mass: 47333.520 Da / Num. of mol.: 1 / Fragment: HA3b
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: type C / Plasmid: pMAL-cRI / Production host: Escherichia coli (E. coli) / References: UniProt: P46085
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 5.2961 Å3/Da / Density % sol: 76.77536 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 1.2M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 44256 / % possible obs: 100 % / Redundancy: 50.9 % / Biso Wilson estimate: 51.6 Å2 / Rsym value: 0.057
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 5.9 / Rsym value: 0.311 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A ROUGH MODEL BUILED BY MAD DATA SET

Resolution: 2.6→47 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2346465.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.243 4449 10.1 %RANDOM
Rwork0.222 ---
obs0.222 44238 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7214 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 57.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.29 Å20 Å20 Å2
2--5.29 Å20 Å2
3----10.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 0 228 5013
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 753 10.4 %
Rwork0.284 6491 -
obs--99.1 %
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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