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- PDB-5ghe: Crystal Structure of Bacillus thuringiensis Cry6Aa2 Protoxin -

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Basic information

Entry
Database: PDB / ID: 5ghe
TitleCrystal Structure of Bacillus thuringiensis Cry6Aa2 Protoxin
ComponentsPesticidal crystal protein Cry6Aa
KeywordsTOXIN / Cry6Aa2 / ClyA-type / Bacillus thuringiensis
Function / homologysporulation resulting in formation of a cellular spore / toxin activity / killing of cells of another organism / host cell plasma membrane / extracellular region / membrane / Pesticidal crystal protein Cry6Aa
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsHuang, J. / Guan, Z. / Zou, T. / Sun, M. / Yin, P.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of Cry6Aa: A novel nematicidal ClyA-type alpha-pore-forming toxin from Bacillus thuringiensis
Authors: Huang, J. / Guan, Z. / Wan, L. / Zou, T. / Sun, M.
History
DepositionJun 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pesticidal crystal protein Cry6Aa


Theoretical massNumber of molelcules
Total (without water)48,2331
Polymers48,2331
Non-polymers00
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.637, 101.637, 78.905
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Pesticidal crystal protein Cry6Aa / Crystaline entomocidal protoxin / Crystal protein / Insecticidal delta-endotoxin CryVIA(a)


Mass: 48232.969 Da / Num. of mol.: 1 / Fragment: UNP residues 1-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry6Aa, cryVIa, cryVIA(a) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45757
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Glycerol, PEG 100, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. obs: 36545 / % possible obs: 99.8 % / Redundancy: 11.3 % / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
HKL-2000data processing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→44.01 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 1820 4.99 %
Rwork0.1674 --
obs0.1687 36506 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 0 379 3430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073104
X-RAY DIFFRACTIONf_angle_d0.7624202
X-RAY DIFFRACTIONf_dihedral_angle_d12.6821896
X-RAY DIFFRACTIONf_chiral_restr0.048480
X-RAY DIFFRACTIONf_plane_restr0.005548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9006-1.9520.27671130.23082669X-RAY DIFFRACTION98
1.952-2.00940.21431490.19512642X-RAY DIFFRACTION100
2.0094-2.07430.24271450.18182672X-RAY DIFFRACTION100
2.0743-2.14840.20511260.17092648X-RAY DIFFRACTION100
2.1484-2.23440.18491350.16652639X-RAY DIFFRACTION100
2.2344-2.33610.20951420.1672669X-RAY DIFFRACTION100
2.3361-2.45930.23051340.17262668X-RAY DIFFRACTION100
2.4593-2.61330.20071090.17852710X-RAY DIFFRACTION100
2.6133-2.81510.21071590.17812645X-RAY DIFFRACTION100
2.8151-3.09830.21211520.17282657X-RAY DIFFRACTION100
3.0983-3.54650.20891480.15942668X-RAY DIFFRACTION100
3.5465-4.46750.1571810.14072653X-RAY DIFFRACTION100
4.4675-44.02190.14381270.16152746X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -31.7249 Å / Origin y: -11.4247 Å / Origin z: -0.7188 Å
111213212223313233
T0.0932 Å2-0.0036 Å20.0242 Å2-0.0752 Å20.0067 Å2--0.1072 Å2
L1.9708 °2-0.3635 °21.4228 °2-0.4504 °2-0.2703 °2--1.5595 °2
S0.0008 Å °0.0766 Å °0.0255 Å °0.0052 Å °-0.0088 Å °0.0021 Å °0.0045 Å °0.0088 Å °0.0229 Å °
Refinement TLS groupSelection details: all

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