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- PDB-6owk: Crystal structure of a Bacillus thuringiensis Cry1B.867 tryptic c... -

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Basic information

Entry
Database: PDB / ID: 6owk
TitleCrystal structure of a Bacillus thuringiensis Cry1B.867 tryptic core variant
ComponentsPesticidal crystal protein Cry1Be, Cry1K-like protein chimera
KeywordsTOXIN / Bacillus thuringiensis / Cry toxin / B.t.
Function / homology
Function and homology information


symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity / signaling receptor binding
Similarity search - Function
Pesticidal crystal protein Cry1Aa, domain IV / : / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein, central domain superfamily ...Pesticidal crystal protein Cry1Aa, domain IV / : / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal / delta endotoxin / Pesticidal crystal protein / Pesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily / delta endotoxin, N-terminal domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Delta-Endotoxin; domain 1 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Pesticidal crystal protein Cry1Be / Pesticidal crystal protein Cry1Ka / Crystaline entomocidal protoxin
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.698 Å
AuthorsRydel, T.J. / Evdokimov, A. / Beishir, S.C.
CitationJournal: Appl.Environ.Microbiol. / Year: 2019
Title: Bacillus thuringiensis Cry1Da_7 and Cry1B.868 Protein Interactions with Novel Receptors Allow Control of Resistant Fall Armyworms, Spodoptera frugiperda (J.E. Smith).
Authors: Wang, Y. / Wang, J. / Fu, X. / Nageotte, J.R. / Silverman, J. / Bretsnyder, E.C. / Chen, D. / Rydel, T.J. / Bean, G.J. / Li, K.S. / Kraft, E. / Gowda, A. / Nance, A. / Moore, R.G. / Pleau, M. ...Authors: Wang, Y. / Wang, J. / Fu, X. / Nageotte, J.R. / Silverman, J. / Bretsnyder, E.C. / Chen, D. / Rydel, T.J. / Bean, G.J. / Li, K.S. / Kraft, E. / Gowda, A. / Nance, A. / Moore, R.G. / Pleau, M.J. / Milligan, J.S. / Anderson, H.M. / Asiimwe, P. / Evans, A. / Moar, W.J. / Martinelli, S. / Head, G.P. / Haas, J.A. / Baum, J.A. / Yang, F. / Kerns, D.L. / Jerga, A.
History
DepositionMay 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera


Theoretical massNumber of molelcules
Total (without water)69,7141
Polymers69,7141
Non-polymers00
Water00
1
A: Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera

A: Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera

A: Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera


Theoretical massNumber of molelcules
Total (without water)209,1433
Polymers209,1433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6550 Å2
ΔGint-4 kcal/mol
Surface area64350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.176, 106.176, 85.302
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 Pesticidal crystal protein Cry1Be, Cry1K-like protein chimera / 139 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryIB(e)


Mass: 69714.469 Da / Num. of mol.: 1
Fragment: Cry1Be (UNP residues 35-510) + Cry1K (UNP residues 481-621)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry1Be, 158C2B, cryIB(e) / Production host: Bacillus thuringiensis (bacteria) / Variant (production host): 867
References: UniProt: O85805, UniProt: V9I1B1, UniProt: Q45715*PLUS

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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: 2.06 Å3/Da / Density % sol: 40 % / Description: Star of David-shaped, six-sided crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.3 / Details: 20% PEG3350, 0.2 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 6, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.698→38.691 Å / Num. obs: 15172 / % possible obs: 93.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 25.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 4.83 / Num. unique obs: 597 / % possible all: 79.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EB7

3eb7


Resolution: 2.698→38.691 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 1404 9.94 %Random selection
Rwork0.2228 ---
obs0.2284 14128 93.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.698→38.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 0 0 4664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044776
X-RAY DIFFRACTIONf_angle_d0.7686507
X-RAY DIFFRACTIONf_dihedral_angle_d4.9972812
X-RAY DIFFRACTIONf_chiral_restr0.046722
X-RAY DIFFRACTIONf_plane_restr0.006848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6979-2.79430.35361150.2991097X-RAY DIFFRACTION80
2.7943-2.90620.35621330.27491163X-RAY DIFFRACTION87
2.9062-3.03840.32121410.25671255X-RAY DIFFRACTION93
3.0384-3.19850.33761460.2581307X-RAY DIFFRACTION97
3.1985-3.39880.30191480.24291335X-RAY DIFFRACTION97
3.3988-3.6610.30911460.23871306X-RAY DIFFRACTION96
3.661-4.02910.28631490.22571318X-RAY DIFFRACTION97
4.0291-4.61130.24841390.19651309X-RAY DIFFRACTION95
4.6113-5.80660.23931420.19241324X-RAY DIFFRACTION96
5.8066-38.69530.22911450.19911310X-RAY DIFFRACTION93

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