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- PDB-3win: Clostridium botulinum Hemagglutinin -

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Basic information

Entry
Database: PDB / ID: 3win
TitleClostridium botulinum Hemagglutinin
Components
  • (HA3) x 2
  • 17 kD hemagglutinin component
  • HA1
KeywordsTOXIN / bacterial pathogenesis / bacterial toxins / carbohydrate-binding protein / E-cadherin / epithelial cell / protein complexes / botulinum toxin / hemagglutinin / Beta-trefoil
Function / homology
Function and homology information


: / extracellular region
Similarity search - Function
: / Hemagglutinin component HA-17 / Jelly Rolls - #1090 / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Proaerolysin; Chain A, domain 3 - #20 / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Clostridium enterotoxin / Ricin-type beta-trefoil lectin domain-like ...: / Hemagglutinin component HA-17 / Jelly Rolls - #1090 / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Proaerolysin; Chain A, domain 3 - #20 / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Clostridium enterotoxin / 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 / Beta Complex / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
HA1 / HA3 / 17 kD hemagglutinin component
Similarity search - Component
Biological speciesClostridium botulinum B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsAmatsu, S. / Sugawara, Y. / Matsumura, T. / Fujinaga, Y. / Kitadokoro, K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structure of Clostridium botulinum Whole Hemagglutinin Reveals a Huge Triskelion-shaped Molecular Complex
Authors: Amatsu, S. / Sugawara, Y. / Matsumura, T. / Kitadokoro, K. / Fujinaga, Y.
History
DepositionSep 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations
Revision 1.2Nov 27, 2013Group: Derived calculations
Revision 1.3Dec 25, 2013Group: Database references
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: HA3
E: HA3
C: 17 kD hemagglutinin component
A: HA1
B: HA1


Theoretical massNumber of molelcules
Total (without water)162,4245
Polymers162,4245
Non-polymers00
Water90150
1
D: HA3
E: HA3
C: 17 kD hemagglutinin component
A: HA1
B: HA1

D: HA3
E: HA3
C: 17 kD hemagglutinin component
A: HA1
B: HA1

D: HA3
E: HA3
C: 17 kD hemagglutinin component
A: HA1
B: HA1


Theoretical massNumber of molelcules
Total (without water)487,27115
Polymers487,27115
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Unit cell
Length a, b, c (Å)324.726, 324.726, 117.588
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein HA3


Mass: 22295.070 Da / Num. of mol.: 1 / Fragment: UNP residues 7-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum B (bacteria) / Gene: ha3 / Plasmid: pET52b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q33CP8
#2: Protein HA3


Mass: 48761.977 Da / Num. of mol.: 1 / Fragment: UNP residues 2-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum B (bacteria) / Gene: ha3 / Plasmid: pET52b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q33CP8
#3: Protein 17 kD hemagglutinin component / HA2


Mass: 19248.541 Da / Num. of mol.: 1 / Fragment: UNP residues 19-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum B (bacteria) / Gene: hem17/B, ha2 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45841
#4: Protein HA1


Mass: 36059.090 Da / Num. of mol.: 2 / Fragment: UNP residues 196-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum B (bacteria) / Gene: ha1 / Plasmid: pET52b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q33CP6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 5.51 Å3/Da / Density % sol: 77.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.25M ammonium chloride, 3%(w/v) polyethylene glycol 4000, 3% trehalose, 3%(w/v) benzamidine HCl, 3%(w/v) methylpentanediol, 3%(w/v) ethylene glycol, 0.1M calcium chloride, 0.1M Tris-HCl , ...Details: 0.25M ammonium chloride, 3%(w/v) polyethylene glycol 4000, 3% trehalose, 3%(w/v) benzamidine HCl, 3%(w/v) methylpentanediol, 3%(w/v) ethylene glycol, 0.1M calcium chloride, 0.1M Tris-HCl , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 45595 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 83.2 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.494 / Num. unique all: 4478 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E4M

2e4m


Resolution: 3.5→48.43 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.867 / SU B: 41.489 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 2.112 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 2323 5.1 %RANDOM
Rwork0.19992 ---
obs0.2025 43265 98.25 %-
all-45595 --
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: 113.213 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10472 0 0 50 10522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0210687
X-RAY DIFFRACTIONr_bond_other_d0.0010.029931
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.93814544
X-RAY DIFFRACTIONr_angle_other_deg0.894322753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.04151294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.85525.564550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.361151781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2061538
X-RAY DIFFRACTIONr_chiral_restr0.0940.21620
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022617
X-RAY DIFFRACTIONr_mcbond_it5.1978.425191
X-RAY DIFFRACTIONr_mcbond_other5.1978.425190
X-RAY DIFFRACTIONr_mcangle_it8.31112.6316480
X-RAY DIFFRACTIONr_mcangle_other8.3112.6316481
X-RAY DIFFRACTIONr_scbond_it5.3428.8055494
X-RAY DIFFRACTIONr_scbond_other5.3428.8055495
X-RAY DIFFRACTIONr_scangle_other8.62413.0378065
X-RAY DIFFRACTIONr_long_range_B_refined12.26568.43212772
X-RAY DIFFRACTIONr_long_range_B_other12.26368.43212772
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 165 -
Rwork0.306 3140 -
obs--98.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.04110.3747-0.73342.0019-0.18860.2020.1411-0.15630.1767-0.1137-0.102-0.374-0.06860.0477-0.03910.10760.00930.0520.0797-0.02020.107411.6691399.1961116.7801
22.1288-1.645-0.09851.60680.09650.03450.05410.11430.14660.0097-0.0008-0.18250.02830.0459-0.05330.13090.1067-0.06460.1491-0.08670.083942.1105357.4383115.6159
33.8863-1.2061.2593.78130.62991.50540.12850.3661-0.3101-0.4646-0.18680.32460.0095-0.03110.05820.27090.1014-0.13410.3483-0.26240.214669.6486316.2478112.9515
40.8199-0.1624-0.09013.7808-0.25952.3062-0.0962-0.2861-0.06370.43930.0988-0.6230.49010.2466-0.00260.33770.1648-0.20.3203-0.25820.477390.893280.3671134.3869
51.3160.57360.96670.79321.50884.41960.0468-0.1323-0.25770.3088-0.0678-0.0540.4781-0.24770.0210.24720.0605-0.07640.1172-0.11220.243578.1963308.6031160.3693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D22 - 188
2X-RAY DIFFRACTION2E208 - 626
3X-RAY DIFFRACTION3C5 - 145
4X-RAY DIFFRACTION4A9 - 294
5X-RAY DIFFRACTION5B9 - 294

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