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- PDB-3ron: Crystal Structure and Hemolytic Activity of the Cyt1Aa Toxin from... -

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Basic information

Entry
Database: PDB / ID: 3ron
TitleCrystal Structure and Hemolytic Activity of the Cyt1Aa Toxin from Bacillus thuringiensis subsp. israelensis
ComponentsType-1Aa cytolytic delta-endotoxin
KeywordsCELL INVASION / Structural Genomics / Israel Structural Proteomics Center / ISPC / cytolysin fold
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / toxin activity / extracellular region
Similarity search - Function
Delta-endotoxin CytB / Delta-endotoxin CytB-like / Delta-endotoxin CytB / Delta-endotoxin CytB-like superfamily / Bacillus thuringiensis toxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Type-1Aa cytolytic delta-endotoxin
Similarity search - Component
Biological speciesBacillus thuringiensis serovar israelensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsCohen, S. / Albeck, S. / Ben-Dov, E. / Cahan, R. / Firer, M. / Zaritsky, A. / Dym, O. / Israel Structural Proteomics Center (ISPC)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Cyt1Aa Toxin: Crystal Structure Reveals Implications for Its Membrane-Perforating Function.
Authors: Cohen, S. / Albeck, S. / Ben-Dov, E. / Cahan, R. / Firer, M. / Zaritsky, A. / Dym, O.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Sep 13, 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: Type-1Aa cytolytic delta-endotoxin
B: Type-1Aa cytolytic delta-endotoxin


Theoretical massNumber of molelcules
Total (without water)54,7102
Polymers54,7102
Non-polymers00
Water55831
1
A: Type-1Aa cytolytic delta-endotoxin


Theoretical massNumber of molelcules
Total (without water)27,3551
Polymers27,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type-1Aa cytolytic delta-endotoxin


Theoretical massNumber of molelcules
Total (without water)27,3551
Polymers27,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.895, 65.822, 176.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type-1Aa cytolytic delta-endotoxin / 27 kDa cytolytic toxin


Mass: 27354.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar israelensis (bacteria)
Gene: cyt1Aa, cytA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A382
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.8 Å3/Da / Density % sol: 31.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: of 20% PEG 6000, 0.1 M NaAcetate pH 5.0 and 0.2 M NH4Cl, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 22, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 21208 / Num. obs: 20996 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.19→2.24 Å / % possible all: 92.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RCI

2rci


Resolution: 2.19→7.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.092 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26068 1044 5.1 %RANDOM
Rwork0.1953 ---
all0.1987 ---
obs0.1987 19384 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.622 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.19→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 0 31 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223178
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2121.9394343
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.2155404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.73727.021141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56115518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.317152
X-RAY DIFFRACTIONr_chiral_restr0.1560.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212378
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1381.52024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07823302
X-RAY DIFFRACTIONr_scbond_it3.52731154
X-RAY DIFFRACTIONr_scangle_it5.4984.51041
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.191→2.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 71 -
Rwork0.255 1239 -
obs--90.03 %

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