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- PDB-1ciy: INSECTICIDAL TOXIN: STRUCTURE AND CHANNEL FORMATION -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1ciy
TitleINSECTICIDAL TOXIN: STRUCTURE AND CHANNEL FORMATION
ComponentsCRYIA(A)
KeywordsTOXIN / DELTA-ENDOTOXIN CRYIA(A) / ICP
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
: / Pesticidal crystal protein Cry1Aa, domain IV / : / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, N-terminal domain ...: / Pesticidal crystal protein Cry1Aa, domain IV / : / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, N-terminal domain / 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 / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Delta-Endotoxin; domain 1 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Pesticidal crystal protein Cry1Aa
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsGrochulski, P. / Cygler, M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Bacillus thuringiensis CryIA(a) insecticidal toxin: crystal structure and channel formation.
Authors: Grochulski, P. / Masson, L. / Borisova, S. / Pusztai-Carey, M. / Schwartz, J.L. / Brousseau, R. / Cygler, M.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Lepidopteran-Specific Insecticidal Crystal Protein Cryla(A)
Authors: Borisova, S. / Grochulski, P. / Van Faassen, H. / Pusztai-Carey, M. / Masson, L. / Cygler, M.
#2: Journal: Nature / Year: 1991
Title: Crystal Structure of Insecticidal Delta-Endotoxin from Bacillus Thuringiensis at 2.5 A Resolution
Authors: Li, J.D. / Carroll, J. / Ellar, D.J.
History
DepositionJun 1, 1995Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.pdbx_collection_date / _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: CRYIA(A)


Theoretical massNumber of molelcules
Total (without water)66,1671
Polymers66,1671
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.000, 111.500, 154.600
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 CRYIA(A)


Mass: 66166.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: HD-1 / Variant: KURSTAKI / Plasmid: PUC8 PROTEIN PURIFIED FROM / Production host: Escherichia coli (E. coli) / References: UniProt: P0A366
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.53 Å3/Da / Density % sol: 55 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 10 / Method: vapor diffusion / Details: Borisova, S., (1994) J.Mol.Biol., 243, 530.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
220-30 mMCAPS1drop
33-4 %MPD1drop
410 %MPD1reservoir
5100 mMCAPS1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→154 Å / Num. obs: 33090 / % possible obs: 74 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Num. measured all: 86937

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.25→8 Å / σ(F): 4
RfactorNum. reflection% reflection
Rfree0.248 --
Rwork0.163 --
obs0.163 32000 73 %
Displacement parametersBiso mean: 27.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4568 0 0 122 4690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.48
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Rfactor all: 0.21 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.93
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.48

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