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- PDB-2rci: High-resolution crystal structure of activated Cyt2Ba monomer fro... -

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Basic information

Entry
Database: PDB / ID: 2rci
TitleHigh-resolution crystal structure of activated Cyt2Ba monomer from Bacillus thuringiensis subsp. israelensis
ComponentsType-2Ba cytolytic delta-endotoxin
KeywordsTOXIN / alpha/beta architecture with beta-sheet surrounded by two alpha-helix layers / Structural Genomics / Israel Structural Proteomics Center / ISPC / Plasmid / Sporulation
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-2Ba cytolytic delta-endotoxin
Similarity search - Component
Biological speciesBacillus thuringiensis serovar israelensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDym, O. / Israel Structural Proteomics Center (ISPC)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: High-resolution crystal structure of activated Cyt2Ba monomer from Bacillus thuringiensis subsp. israelensis.
Authors: Cohen, S. / Dym, O. / Albeck, S. / Ben-Dov, E. / Cahan, R. / Firer, M. / Zaritsky, A.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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-2Ba cytolytic delta-endotoxin


Theoretical massNumber of molelcules
Total (without water)22,9731
Polymers22,9731
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.481, 43.259, 55.650
Angle α, β, γ (deg.)90.00, 112.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-239-

HOH

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Components

#1: Protein Type-2Ba cytolytic delta-endotoxin / 29 kDa cytolytic toxin


Mass: 22973.137 Da / Num. of mol.: 1 / Fragment: Residues 35-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar israelensis (bacteria)
Strain: 4Q2, T301 / Gene: cyt2Ba1, cyt2Ba7, cytB / Production host: Escherichia coli (E. coli) / References: UniProt: Q45723
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: 1M Na/K Tartrate, 0.1M Tris-HCl pH 7.0, 0.2M Li2SO4, MICROBATCH, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 16805 / Num. obs: 16805 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.075 / Rsym value: 0.103 / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CBY

1cby


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.409 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21613 849 5.1 %RANDOM
Rwork0.18696 ---
obs0.1884 15956 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.831 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å21.42 Å2
2--0.05 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 0 112 1609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221530
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9292089
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8252670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80515261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.812153
X-RAY DIFFRACTIONr_chiral_restr0.1090.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021137
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2741
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21092
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8651.5977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40821550
X-RAY DIFFRACTIONr_scbond_it2.3363636
X-RAY DIFFRACTIONr_scangle_it3.6054.5537
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 47 -
Rwork0.25 1080 -
obs--90.38 %

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