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- PDB-4w8j: Structure of the full-length insecticidal protein Cry1Ac reveals ... -

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Basic information

Entry
Database: PDB / ID: 4w8j
TitleStructure of the full-length insecticidal protein Cry1Ac reveals intriguing details of toxin packaging into in vivo formed crystals
ComponentsPesticidal crystal protein cry1Ac
KeywordsTOXIN / insecticidal / pore forming / protoxin
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 Cry1Ac
Similarity search - Component
Biological speciesBacillus thuringiensis serovar kurstaki str. HD73 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsEvdokimov, A.G. / Moshiri, F. / Sturman, E.J. / Rydel, T.J. / Zheng, M. / Seale, J.W. / Franklin, S.
CitationJournal: Protein Sci. / Year: 2014
Title: Structure of the full-length insecticidal protein Cry1Ac reveals intriguing details of toxin packaging into in vivo formed crystals.
Authors: Evdokimov, A.G. / Moshiri, F. / Sturman, E.J. / Rydel, T.J. / Zheng, M. / Seale, J.W. / Franklin, S.
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pesticidal crystal protein cry1Ac
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1385
Polymers133,9811
Non-polymers1574
Water90150
1
A: Pesticidal crystal protein cry1Ac
hetero molecules

A: Pesticidal crystal protein cry1Ac
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,27710
Polymers267,9622
Non-polymers3158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6030 Å2
ΔGint-38 kcal/mol
Surface area88100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.314, 87.314, 266.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Pesticidal crystal protein cry1Ac


Mass: 133981.031 Da / Num. of mol.: 1
Mutation: C661S,C730S,C796S,C802S,C814S,C816S,C822S,C837S,C990S,C1025S,C1045S,C1063S,C1076S,C1125S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki str. HD73 (bacteria)
Gene: HD73_6004 / Plasmid: pCry1Ac
Details (production host): sporulation promoter, chloramphenicol resistance
Production host: Bacillus thuringiensis (bacteria) / Strain (production host): EG10650 / References: UniProt: M4LET9, UniProt: P05068*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.89 Å3/Da / Density % sol: 35.09 % / Description: tetragonal bipyramid
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.84
Details: 600 nL of 13 mg/mL protein in 20 mM ethanolamine buffer with 0.35 M NaCl was mixed with 600 nL of 700 mM sodium-potassium tartrate, 100 mM BIS-TRIS propane pH 7.84 and 120 nL of 9 mM n-decyl ...Details: 600 nL of 13 mg/mL protein in 20 mM ethanolamine buffer with 0.35 M NaCl was mixed with 600 nL of 700 mM sodium-potassium tartrate, 100 mM BIS-TRIS propane pH 7.84 and 120 nL of 9 mM n-decyl thiomaltoside, and the resulting 1.2 uL sitting drop was allowed to equili- brate against 80uL of the tartrate/BIS-TRIS propane reservoir solution at 19C.
PH range: 7.8-7.9

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2011
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→87 Å / Num. obs: 26818 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.8
Reflection shellResolution: 2.78→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house

Resolution: 2.78→82.97 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.85 / SU B: 18.927 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.539 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33226 1340 5 %RANDOM
Rwork0.22645 ---
obs0.23173 25202 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.344 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.96 Å2
Refinement stepCycle: 1 / Resolution: 2.78→82.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8152 0 4 50 8206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228335
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.93811317
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98651009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59123.912432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.05151357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5341564
X-RAY DIFFRACTIONr_chiral_restr0.0950.21240
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216461
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5951.55047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14728166
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.57833288
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8044.53151
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.783→2.855 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 89 -
Rwork0.266 1842 -
obs--99.59 %

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