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- PDB-5kuc: Crystal structure of trypsin activated Cry6Aa -

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Basic information

Entry
Database: PDB / ID: 5kuc
TitleCrystal structure of trypsin activated Cry6Aa
ComponentsPesticidal crystal protein Cry6Aa
KeywordsTOXIN / pesticidal / pore formation
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKelker, M.S. / Xu, X. / Lee, M. / Chan, M. / Hung, S. / Dementiev, K. / Hey, T. / Chikwana, V.M. / Narva, K.E.
CitationJournal: Bmc Biol. / Year: 2016
Title: The pesticidal Cry6Aa toxin from Bacillus thuringiensis is structurally similar to HlyE-family alpha pore-forming toxins.
Authors: Dementiev, A. / Board, J. / Sitaram, A. / Hey, T. / Kelker, M.S. / Xu, X. / Hu, Y. / Vidal-Quist, C. / Chikwana, V. / Griffin, S. / McCaskill, D. / Wang, N.X. / Hung, S.C. / Chan, M.K. / ...Authors: Dementiev, A. / Board, J. / Sitaram, A. / Hey, T. / Kelker, M.S. / Xu, X. / Hu, Y. / Vidal-Quist, C. / Chikwana, V. / Griffin, S. / McCaskill, D. / Wang, N.X. / Hung, S.C. / Chan, M.K. / Lee, M.M. / Hughes, J. / Wegener, A. / Aroian, R.V. / Narva, K.E. / Berry, C.
History
DepositionJul 13, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionAug 3, 2016ID: 5J65
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pesticidal crystal protein Cry6Aa


Theoretical massNumber of molelcules
Total (without water)54,1311
Polymers54,1311
Non-polymers00
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.967, 112.967, 76.627
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: 54131.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry6Aa, cryVIa, cryVIA(a) / Production host: Pseudomonas fluorescens (bacteria) / References: UniProt: Q45757
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Cry6Aa protein crystals were grown at 291 K from sitting drops containing the protein sample and reservoir solution (20% (w/v) PEG 1000, 0.1 M sodium phosphate dibasic/citric acid pH 4.2; 0.2 M lithium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12675 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2011 / Details: Diamonds Laue with Beryllium lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12675 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 37186 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 33.41
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.229

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NRJ

2nrj


Resolution: 2→30.01 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36
RfactorNum. reflection% reflection
Rfree0.228 1870 5.03 %
Rwork0.1877 --
obs-37151 98.8 %
Refinement stepCycle: LAST / Resolution: 2→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 0 422 3605

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