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- PDB-4moa: Crystal structure of CRY4BA-R203Q TOXIN -

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Basic information

Entry
Database: PDB / ID: 4moa
TitleCrystal structure of CRY4BA-R203Q TOXIN
ComponentsPesticidal crystal protein cry4Ba
KeywordsTOXIN / PESTICIDAL PROTEIN
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
: / Cry1Ac, domain VII / 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 ...: / Cry1Ac, domain VII / 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 Cry4Ba
Similarity search - Component
Biological speciesBacillus thuringiensis serovar israelensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThamwiriyasati, N. / Angsuthanasombat, C. / Chen, C.-J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Potential Prepore Trimer Formation by the Bacillus thuringiensis Mosquito-specific Toxin: MOLECULAR INSIGHTS INTO A CRITICAL PREREQUISITE OF MEMBRANE-BOUND MONOMERS
Authors: Sriwimol, W. / Aroonkesorn, A. / Sakdee, S. / Kanchanawarin, C. / Uchihashi, T. / Ando, T. / Angsuthanasombat, C.
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pesticidal crystal protein cry4Ba


Theoretical massNumber of molelcules
Total (without water)67,6751
Polymers67,6751
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pesticidal crystal protein cry4Ba
x 6


Theoretical massNumber of molelcules
Total (without water)406,0506
Polymers406,0506
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_554y,x,-z-11
crystal symmetry operation5_554x-y,-y,-z-11
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area14900 Å2
ΔGint-102 kcal/mol
Surface area140060 Å2
MethodPISA
3
A: Pesticidal crystal protein cry4Ba

A: Pesticidal crystal protein cry4Ba

A: Pesticidal crystal protein cry4Ba


Theoretical massNumber of molelcules
Total (without water)203,0253
Polymers203,0253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6270 Å2
ΔGint-44 kcal/mol
Surface area71210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.618, 184.618, 187.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Pesticidal crystal protein cry4Ba / 128 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryIVB(a)


Mass: 67674.953 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 40-641 / Mutation: R203Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar israelensis (bacteria)
Gene: cry4Ba, bt8, cryD2, cryIVB(a), isrH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P05519
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 4.54 Å3/Da / Density % sol: 72.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M ammonium acetate, 0.01M MgCl2, 10%(v/v) MPD, 0.05M Tris HCl buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Sep 12, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 82325 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1w99

1w99


Resolution: 2→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 7843 -RANDOM
Rwork0.2159 ---
obs0.22 78493 95.2 %-
all-78492 --
Solvent computationBsol: 63.383 Å2
Displacement parametersBiso max: 149.79 Å2 / Biso mean: 30.044 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.983 Å20 Å20 Å2
2--1.983 Å20 Å2
3----3.967 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 0 282 5056
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_deg1.33
LS refinement shellResolution: 2→2.07 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param

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