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- PDB-5b2h: Crystal structure of HA33 from Clostridium botulinum serotype C s... -

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Basic information

Entry
Database: PDB / ID: 5b2h
TitleCrystal structure of HA33 from Clostridium botulinum serotype C strain Yoichi
ComponentsHA-33
KeywordsSUGAR BINDING PROTEIN / Hemagglutinin
Function / homology
Function and homology information


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
TRIETHYLENE GLYCOL / HA-33
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAkiyama, T. / Hayashi, S. / Matsumoto, T. / Hasegawa, K. / Yamano, A. / Suzuki, T. / Niwa, K. / Watanabe, T. / Sagane, Y. / Yajima, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Conformational divergence in the HA-33/HA-17 trimer of serotype C and D botulinum toxin complex
Authors: Sagane, Y. / Hayashi, S. / Akiyama, T. / Matsumoto, T. / Hasegawa, K. / Yamano, A. / Suzuki, T. / Niwa, K. / Watanabe, T. / Yajima, S.
History
DepositionJan 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 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
Item: _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: HA-33
B: HA-33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8433
Polymers65,6932
Non-polymers1501
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-4 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.517, 142.517, 126.794
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein HA-33


Mass: 32846.363 Da / Num. of mol.: 2 / Fragment: UNP residues 3-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: C-Yoichi / Gene: ha-33 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93HT5
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3.77 Å3/Da / Density % sol: 67.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-HCl, 5% PEG400, 8% PEG 8000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 9, 2013
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. obs: 48719 / % possible obs: 100 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.062 / Rrim(I) all: 0.106 / Χ2: 1.388 / Net I/av σ(I): 15.477 / Net I/σ(I): 8.8 / Num. measured all: 141410
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.242.80.46124160.6890.3380.5741.36699.8
2.24-2.282.90.48124100.6980.3520.5971.276100
2.28-2.322.90.43624720.7690.3180.5421.37100
2.32-2.372.90.40124390.7690.2930.4991.342100
2.37-2.422.90.35824290.830.2630.4461.369100
2.42-2.482.90.30724490.8620.2230.381.346100
2.48-2.542.90.2524370.9060.1820.3111.281100
2.54-2.612.90.21324250.9250.1550.2641.338100
2.61-2.692.90.20124560.9330.1460.251.303100
2.69-2.772.90.18324200.9460.1340.2281.381100
2.77-2.872.90.14124400.9680.1020.1751.269100
2.87-2.992.90.1124650.9790.080.1371.323100
2.99-3.122.90.09324160.9840.0680.1161.453100
3.12-3.292.90.07624540.9880.0550.0951.351100
3.29-3.492.90.05924120.9920.0420.0721.384100
3.49-3.762.90.05524340.9940.0390.0681.589100
3.76-4.142.90.04524350.9950.0320.0551.583100
4.14-4.742.90.03824520.9960.0270.0461.66999.9
4.74-5.972.90.03724300.9970.0270.0461.311100
5.97-502.90.03624280.9970.0260.0451.44699.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E4M

2e4m


Resolution: 2.2→30.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.715 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 2464 5.1 %RANDOM
Rwork0.1844 ---
obs0.1858 46254 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.36 Å2 / Biso mean: 33.575 Å2 / Biso min: 14.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å20 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 2.2→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 10 305 4946
Biso mean--29.04 33.13 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024756
X-RAY DIFFRACTIONr_bond_other_d0.0060.024335
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9026467
X-RAY DIFFRACTIONr_angle_other_deg0.93439918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8095568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.46626.126253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47715814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0731512
X-RAY DIFFRACTIONr_chiral_restr0.080.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021222
X-RAY DIFFRACTIONr_mcbond_it1.9123.2752272
X-RAY DIFFRACTIONr_mcbond_other1.9123.2742271
X-RAY DIFFRACTIONr_mcangle_it3.0644.9012840
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 179 -
Rwork0.238 3434 -
all-3613 -
obs--99.86 %

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