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- PDB-4qx2: Cry3A Toxin structure obtained by injecting Bacillus thuringiensi... -

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Basic information

Entry
Database: PDB / ID: 4qx2
TitleCry3A Toxin structure obtained by injecting Bacillus thuringiensis cells in an XFEL beam, collecting data by serial femtosecond crystallographic methods and processing data with the cctbx.xfel software suite
ComponentsPesticidal crystal protein cry3Aa
KeywordsTOXIN / in vivo crystals / microcrystals / serial femtosecond crystallography / SFX / LCLS / X-ray Free-electron laser / insecticidal toxin
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, central domain superfamily / Pesticidal crystal protein, N-terminal domain / 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, central domain superfamily / Pesticidal crystal protein, N-terminal domain / 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 serovar tenebrionis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsSawaya, M.R. / Cascio, D. / Gingery, M. / Rodriguez, J. / Goldschmidt, L. / Colletier, J.-P. / Messerschmidt, M. / Boutet, S. / Koglin, J.E. / Williams, G.J. ...Sawaya, M.R. / Cascio, D. / Gingery, M. / Rodriguez, J. / Goldschmidt, L. / Colletier, J.-P. / Messerschmidt, M. / Boutet, S. / Koglin, J.E. / Williams, G.J. / Brewster, A.S. / Nass, K. / Hattne, J. / Botha, S. / Doak, R.B. / Shoeman, R.L. / DePonte, D.P. / Park, H.-W. / Federici, B.A. / Sauter, N.K. / Schlichting, I. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Protein crystal structure obtained at 2.9 angstrom resolution from injecting bacterial cells into an X-ray free-electron laser beam.
Authors: Sawaya, M.R. / Cascio, D. / Gingery, M. / Rodriguez, J. / Goldschmidt, L. / Colletier, J.P. / Messerschmidt, M.M. / Boutet, S. / Koglin, J.E. / Williams, G.J. / Brewster, A.S. / Nass, K. / ...Authors: Sawaya, M.R. / Cascio, D. / Gingery, M. / Rodriguez, J. / Goldschmidt, L. / Colletier, J.P. / Messerschmidt, M.M. / Boutet, S. / Koglin, J.E. / Williams, G.J. / Brewster, A.S. / Nass, K. / Hattne, J. / Botha, S. / Doak, R.B. / Shoeman, R.L. / DePonte, D.P. / Park, H.W. / Federici, B.A. / Sauter, N.K. / Schlichting, I. / Eisenberg, D.S.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pesticidal crystal protein cry3Aa


Theoretical massNumber of molelcules
Total (without water)66,6021
Polymers66,6021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.050, 134.760, 104.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Pesticidal crystal protein cry3Aa / 73 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryIIIA(a) ...73 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryIIIA(a) / delta endotoxin Cry3A


Mass: 66602.039 Da / Num. of mol.: 1 / Fragment: UNP residues 58-644
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar tenebrionis (bacteria)
Strain: tenebrionis / Gene: bt13, cry3A, cry3Aa, cryC, cryIIIa, cryIIIA(a) / Plasmid: pPFT3As
Production host: Bacillus thuringiensis subsp. israelensis (bacteria)
Strain (production host): 4Q7 / References: UniProt: P0A379

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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: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 303 K / Method: in vivo crystallization
Details: Cry3A crystallized within the bacterial cell, IN VIVO CRYSTALLIZATION, temperature 303K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.457 Å
DetectorType: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Mar 11, 2013
RadiationMonochromator: no monochromator, FEL beam with 20-30 eV bandwidth
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.457 Å / Relative weight: 1
ReflectionResolution: 2.9→52.42 Å / Num. all: 18583 / Num. obs: 18583 / % possible obs: 92.3 % / Redundancy: 252.5 % / Biso Wilson estimate: 30.55 Å2 / Rmerge(I) obs: 0.216 / Net I/σ(I): 59.2
Reflection shellResolution: 2.9→2.99 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2.3 / % possible all: 39.2

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
cctbx.xfeldata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1DLC

1dlc


Resolution: 2.9→52.42 Å / Cor.coef. Fo:Fc: 0.9225 / Cor.coef. Fo:Fc free: 0.8966 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.864 / SU Rfree Blow DPI: 0.284 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 931 5.01 %RANDOM
Rwork0.1683 ---
obs0.1699 18583 99.14 %-
all-18583 --
Displacement parametersBiso mean: 38.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.6597 Å20 Å20 Å2
2--1.3849 Å20 Å2
3----2.0446 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.9→52.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4659 0 0 0 4659
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014782HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.996511HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1612SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes694HARMONIC5
X-RAY DIFFRACTIONt_it4782HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion18.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion618SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5347SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2823 142 4.98 %
Rwork0.2478 2707 -
all0.2496 2849 -
obs--99.14 %
Refinement TLS params.Method: refined / Origin x: 36.2824 Å / Origin y: 42.4347 Å / Origin z: 46.5065 Å
111213212223313233
T-0.0631 Å2-0.0021 Å20.0344 Å2--0.0852 Å2-0.031 Å2--0.0471 Å2
L1.3167 °20.4388 °20.4618 °2-0.874 °20.1745 °2--0.3993 °2
S-0.0681 Å °0.1121 Å °-0.302 Å °-0.1325 Å °0.1593 Å °-0.1457 Å °-0.0068 Å °-0.0215 Å °-0.0912 Å °
Refinement TLS groupSelection details: { A|* }

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