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- PDB-8w7n: Crystal structure of the in-cell Cry1Aa purified from Bacillus th... -

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Basic information

Entry
Database: PDB / ID: 8w7n
TitleCrystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis
ComponentsPesticidal crystal protein Cry1Aa
KeywordsTOXIN / In cell protein crystal
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
Delta endotoxin / : / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal / delta endotoxin ...Delta endotoxin / : / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / delta endotoxin / 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 / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Pesticidal crystal protein Cry1Aa
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsTanaka, J. / Abe, S. / Hayakawa, T. / Kojima, M. / Yamashita, K. / Hirata, K. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis.
Authors: Tanaka, J. / Abe, S. / Hayakawa, T. / Kojima, M. / Yamashita, K. / Hirata, K. / Ueno, T.
History
DepositionAug 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pesticidal crystal protein Cry1Aa


Theoretical massNumber of molelcules
Total (without water)129,8352
Polymers129,8351
Non-polymers01
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.700, 88.700, 270.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Pesticidal crystal protein Cry1Aa / 133 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryIA(a)


Mass: 129834.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thuringiensis (bacteria) / References: UniProt: P0A367
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 303 K / Method: in cell
Details: Cry1Aa was expressed in the Bt cells by inoculating 250 mL of NYS medium and cultured at 303K for 3 days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 13301 / % possible obs: 100 % / Redundancy: 55.9 % / CC1/2: 0.689 / R split: 0.4754 / Net I/σ(I): 2.5
Reflection shellResolution: 3.6→3.63 Å / Redundancy: 39.9 % / Mean I/σ(I) obs: 1.55 / Num. unique obs: 303 / CC1/2: 0.657 / R split: 0.7328 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata scaling
Coot0.8.9.2model building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→39.82 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.724 / SU B: 62.145 / SU ML: 0.932 / Cross valid method: THROUGHOUT / ESU R Free: 0.934 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31764 668 5.1 %RANDOM
Rwork0.21733 ---
obs0.22246 12547 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å2-0 Å2
2---0.9 Å2-0 Å2
3---1.8 Å2
Refinement stepCycle: 1 / Resolution: 3.6→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8075 0 1 0 8076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0128253
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167629
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.64711209
X-RAY DIFFRACTIONr_angle_other_deg0.3521.56717480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.89751003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.817566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.45101343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022052
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1910.5364036
X-RAY DIFFRACTIONr_mcbond_other0.1910.5364036
X-RAY DIFFRACTIONr_mcangle_it0.3590.9635031
X-RAY DIFFRACTIONr_mcangle_other0.3590.9625032
X-RAY DIFFRACTIONr_scbond_it0.0920.544217
X-RAY DIFFRACTIONr_scbond_other0.0920.544216
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.1980.9936179
X-RAY DIFFRACTIONr_long_range_B_refined0.9655.659211
X-RAY DIFFRACTIONr_long_range_B_other0.9655.659212
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 49 -
Rwork0.251 905 -
obs--100 %

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