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- PDB-7ear: A positively charged mutant Cry3Aa endotoxin -

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Basic information

Entry
Database: PDB / ID: 7ear
TitleA positively charged mutant Cry3Aa endotoxin
ComponentsCrystaline entomocidal protoxin
KeywordsTOXIN / crystal-forming / protein delivery / cell-permeable / endosome-escapable
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 / membrane
Similarity search - Function
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
Crystaline entomocidal protoxin
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, Z. / Lee, M.M. / Chan, M.K.
CitationJournal: Biomaterials / Year: 2021
Title: Efficient intracellular delivery of p53 protein by engineered protein crystals restores tumor suppressing function in vivo.
Authors: Yang, Z. / Lee, M.M.M. / Chan, M.K.
History
DepositionMar 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Crystaline entomocidal protoxin


Theoretical massNumber of molelcules
Total (without water)73,2931
Polymers73,2931
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.840, 132.890, 103.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-911-

HOH

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Components

#1: Protein Crystaline entomocidal protoxin / Pos3Aa


Mass: 73292.977 Da / Num. of mol.: 1
Mutation: N391K,N395K,E423K,Q430K,D432K,E433K,T436K,T461K,D462K,E463K,E466K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry3Aa, EEL55_22485, GH840_26515 / Production host: Bacillus thuringiensis (bacteria) / References: UniProt: Q9S6N9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES/Sodium hydroxide pH7.5, 20% v/v 1,4-butanediol, 200mM Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→66.54 Å / Num. obs: 38330 / % possible obs: 99.92 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.552 / Num. unique obs: 5821 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dlc

1dlc


Resolution: 2.2→66.54 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.914 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1998 5 %RANDOM
Rwork0.1801 ---
obs0.182 38330 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.57 Å2 / Biso mean: 30.035 Å2 / Biso min: 8.77 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.2→66.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 0 216 4914
Biso mean---29.68 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174336
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.6466543
X-RAY DIFFRACTIONr_angle_other_deg1.3531.57410083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4835583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13122.948251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30115803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7781522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021056
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 128 -
Rwork0.232 2829 -
all-2957 -
obs--99.97 %

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