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- PDB-6dj4: Crystal Structure of Bacillus thuringiensis Cry1A.105 Tryptic Core -

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Basic information

Entry
Database: PDB / ID: 6dj4
TitleCrystal Structure of Bacillus thuringiensis Cry1A.105 Tryptic Core
ComponentsCry1A.105
KeywordsTOXIN / Pesticidal crystal protein
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
Crystaline entomocidal protoxin / Pesticidal crystal protein Cry1Ab / Crystaline entomocidal protoxin
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsRydel, T.J. / Sturman, E.J. / Lee, T.C.
CitationJournal: Regul. Toxicol. Pharmacol. / Year: 2018
Title: Safety of the Bacillus thuringiensis-derived Cry1A.105 protein: Evidence that domain exchange preserves mode of action and safety.
Authors: Wang, C. / Li, W. / Kessenich, C.R. / Petrick, J.S. / Rydel, T.J. / Sturman, E.J. / Lee, T.C. / Glenn, K.C. / Edrington, T.C.
History
DepositionMay 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cry1A.105


Theoretical massNumber of molelcules
Total (without water)66,5391
Polymers66,5391
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23030 Å2
Unit cell
Length a, b, c (Å)124.375, 49.441, 103.692
Angle α, β, γ (deg.)90.00, 108.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cry1A.105


Mass: 66539.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cryIA(c) / Production host: Bacillus thuringiensis (bacteria)
References: UniProt: O32306, UniProt: V9I164, UniProt: P0A372*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA perfect matching reference sequence is GenBank accession AGN47973.1

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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: 2.27 Å3/Da / Density % sol: 45.81 % / Description: Rectangular, plate-like
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Crystals were obtained using a precipitant/reservoir solution of 5% (w/v) PEG 4000, 0.1 M sodium citrate buffer, pH 6, and 10% isopropanol. Micro-seeding was required to obtain crystals ...Details: Crystals were obtained using a precipitant/reservoir solution of 5% (w/v) PEG 4000, 0.1 M sodium citrate buffer, pH 6, and 10% isopropanol. Micro-seeding was required to obtain crystals sizable enough for X-ray intensity data collection at the synchrotron.
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→98.25 Å / Num. obs: 11744 / % possible obs: 96.9 % / Redundancy: 3.2 % / Rsym value: 0.139 / Net I/σ(I): 9.9
Reflection shellResolution: 3.01→3.11 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1167 / Rsym value: 0.503 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CryIAa

Resolution: 3.01→49.124 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.97
RfactorNum. reflection% reflection
Rfree0.2791 558 4.75 %
Rwork0.219 --
obs0.2218 11741 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.01→49.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 0 0 27 4578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024667
X-RAY DIFFRACTIONf_angle_d0.5416355
X-RAY DIFFRACTIONf_dihedral_angle_d2.6432739
X-RAY DIFFRACTIONf_chiral_restr0.042696
X-RAY DIFFRACTIONf_plane_restr0.005832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0064-3.30890.3131430.25632736X-RAY DIFFRACTION96
3.3089-3.78760.30751270.23472799X-RAY DIFFRACTION97
3.7876-4.77130.28251450.21372770X-RAY DIFFRACTION96
4.7713-49.13070.25131430.20112878X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3879-0.65940.35530.8650.60331.1727-0.08530.1840.3028-0.09460.0395-0.18180.09860.1826-00.464-0.04170.040.53010.01590.4978-4.8735-0.327716.284
21.8725-0.060.74030.57760.1331.1386-0.0698-0.07050.1859-0.069-0.02050.0930.0287-0.0181-00.45390.01710.03470.3837-0.01250.4178-27.2391-0.51121.0075
30.9034-0.2710.76660.61050.05892.69720.0851-0.2036-0.17020.03810.09770.04110.1707-0.26170.00010.3815-0.05570.02110.41630.02970.4793-33.2851-7.991225.8902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 345 )
3X-RAY DIFFRACTION3chain 'A' and (resid 346 through 609 )

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