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- PDB-1dlc: CRYSTAL STRUCTURE OF INSECTICIDAL DELTA-ENDOTOXIN FROM BACILLUS T... -

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Basic information

Entry
Database: PDB / ID: 1dlc
TitleCRYSTAL STRUCTURE OF INSECTICIDAL DELTA-ENDOTOXIN FROM BACILLUS THURINGIENSIS AT 2.5 ANGSTROMS RESOLUTION
ComponentsDELTA-ENDOTOXIN CRYIIIA
KeywordsTOXIN
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, 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 ...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 Cry3Aa
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLi, J.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: X-Ray Analysis of the Crystalline Parasporal Inclusion in Bacillus Thuringiensis Var. Tenebrionis
Authors: Li, J. / Henderson, R. / Carroll, J. / Ellar, D.
History
DepositionJun 22, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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Assembly

Deposited unit
A: DELTA-ENDOTOXIN CRYIIIA


Theoretical massNumber of molelcules
Total (without water)66,3131
Polymers66,3131
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.090, 134.260, 104.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUE ARG 443 IS MODELED IN TWO CONFORMATIONS.

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Components

#1: Protein DELTA-ENDOTOXIN CRYIIIA


Mass: 66312.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / References: UniProt: P0A379
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CRYIIIA IN THE ATOMIC MODEL IS TAKEN FROM: HOEFTE, H., SEURINCK, J., VAN HOUTVEN, A. ...THE SEQUENCE OF CRYIIIA IN THE ATOMIC MODEL IS TAKEN FROM: HOEFTE, H., SEURINCK, J., VAN HOUTVEN, A. AND VAECK, M. (1987) NUCLEIC ACIDS RES. 15:7183. EMBL ACCESSION NUMBER P07130, ENTRY NAME CR70_BACTT. RESIDUES 1 - 57 ARE REMOVED IN THE MATURE TOXIN. RESIDUES 58 - 60 ARE INVISIBLE IN THE CRYSTAL STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.26 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 9.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlprotein11
20.1 M12NaHCO3
31.2 M12NaBr

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 27727 / Num. measured all: 121767 / Rmerge(I) obs: 0.108

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→16 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.183 -
obs0.183 27726
Refinement stepCycle: LAST / Resolution: 2.5→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 0 106 4803
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_deg1.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.471
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 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.58

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