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- PDB-1cby: DELTA-ENDOTOXIN -

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Basic information

Entry
Database: PDB / ID: 1cby
TitleDELTA-ENDOTOXIN
ComponentsDELTA-ENDOTOXIN CYTB
KeywordsTOXIN / MOSQUITOCIDAL / MEMBRANE PORE / CYTOLYTIC
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-2Aa cytolytic delta-endotoxin
Similarity search - Component
Biological speciesBacillus thuringiensis serovar kyushuensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsLi, J.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structure of the mosquitocidal delta-endotoxin CytB from Bacillus thuringiensis sp. kyushuensis and implications for membrane pore formation.
Authors: Li, J. / Koni, P.A. / Ellar, D.J.
#1: Journal: Proteins / Year: 1995
Title: Crystallization of a Membrane Pore-Forming Protein with Mosquitocidal Activity from Bacillus Thuringiensis Subsp. Kyushuensis
Authors: Li, J. / Koni, P.A. / Ellar, D.J.
#2: Journal: Microbiology (Reading, Engl.) / Year: 1994
Title: Biochemical Characterization of Bacillus Thuringiensis Cytolytic Delta-Endotoxins
Authors: Koni, P.A. / Ellar, D.J.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Cloning and Characterization of a Novel Bacillus Thuringiensis Cytolytic Delta-Endotoxin
Authors: Koni, P.A. / Ellar, D.J.
History
DepositionSep 5, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELTA-ENDOTOXIN CYTB


Theoretical massNumber of molelcules
Total (without water)29,2601
Polymers29,2601
Non-polymers00
Water50428
1
A: DELTA-ENDOTOXIN CYTB

A: DELTA-ENDOTOXIN CYTB


Theoretical massNumber of molelcules
Total (without water)58,5212
Polymers58,5212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area6170 Å2
ΔGint-30 kcal/mol
Surface area18680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.810, 66.810, 170.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DELTA-ENDOTOXIN CYTB


Mass: 29260.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar kyushuensis (bacteria)
Species: Bacillus thuringiensis / Strain: KYUSHUENSIS / Gene: CYTB / Plasmid: PCYTB / Gene (production host): CYTB / Production host: Escherichia coli (E. coli) / References: UniProt: Q04470
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 33 %
Crystal grow
*PLUS
pH: 8.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris-HCl1reservoir
250 mMurea1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.6→19 Å / Num. obs: 7235 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.6→19 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.261 -5 %
Rwork0.197 --
obs0.197 7218 96.2 %
Displacement parametersBiso mean: 32 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.6→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 28 1835
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.494
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.14
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.068
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.14
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.068
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.78 Å / Rfactor Rfree: 0.347 / Rfactor obs: 0.304

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