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- PDB-2c9k: Structure of the functional form of the mosquito-larvicidal Cry4A... -

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Basic information

Entry
Database: PDB / ID: 2c9k
TitleStructure of the functional form of the mosquito-larvicidal Cry4Aa toxin from Bacillus thuringiensis at 2.8 A resolution
ComponentsPESTICIDAL CRYSTAL PROTEIN CRY4AA
KeywordsTOXIN / INSECT TOXIN / BIOINSECTICICIDE / PORE FORMATION / RECEPTOR RECOGNITION / SPORULATION
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / : / toxin activity / signaling receptor binding
Similarity search - Function
Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal / delta endotoxin / Pesticidal crystal protein ...Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein, central domain / delta endotoxin / 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 Cry4Aa
Similarity search - Component
Biological speciesBACILLUS THURINGIENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBoonserm, P. / Mo, M. / Angsuthanasombat, C. / Lescar, J.
CitationJournal: J.Bacteriol. / Year: 2006
Title: Structure of the Functional Form of the Mosquito Larvicidal Cry4Aa Toxin from Bacillus Thuringiensis at 2.8-Angstrom Resolution.
Authors: Boonserm, P. / Mo, M. / Angsuthanasombat, C. / Lescar, J.
History
DepositionDec 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PESTICIDAL CRYSTAL PROTEIN CRY4AA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0202
Polymers69,9021
Non-polymers1181
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.199, 202.069, 98.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2131-

HOH

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Components

#1: Protein PESTICIDAL CRYSTAL PROTEIN CRY4AA / INSECTICIDAL DELTA-ENDOTOXIN CRYIVA(A) / CRYSTALINE ENTOMOCIDAL PROTOXIN / 135 KDA CRYSTAL PROTEIN


Mass: 69902.234 Da / Num. of mol.: 1 / Fragment: RESIDUES 68-679
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS THURINGIENSIS (bacteria) / Strain: ISRAELENSIS (BTI) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P16480
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.6 Å3/Da / Density % sol: 65 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 138542 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W99

1w99


Resolution: 2.8→7 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 235 TO 244 AND 485 TO 488 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND WERE NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1112 5.2 %RANDOM
Rwork0.2025 ---
obs0.2025 21303 100 %-
Solvent computationBsol: 59.1661 Å2 / ksol: 0.445975 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.709 Å20 Å20 Å2
2---17.048 Å20 Å2
3---11.339 Å2
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 8 238 5057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006376
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.27413
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3MPD.PARAM

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