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Yorodumi- PDB-4qx2: Cry3A Toxin structure obtained by injecting Bacillus thuringiensi... -
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-Basic information
Entry | Database: PDB / ID: 4qx2 | ||||||
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Title | Cry3A 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 | ||||||
Components | Pesticidal crystal protein cry3Aa | ||||||
Keywords | TOXIN / 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 | ||||||
Biological species | Bacillus thuringiensis serovar tenebrionis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.9 Å | ||||||
Authors | Sawaya, 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. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qx2.cif.gz | 241 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qx2.ent.gz | 195.2 KB | Display | PDB format |
PDBx/mmJSON format | 4qx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/4qx2 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/4qx2 | HTTPS FTP |
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-Related structure data
Related structure data | 4qx0C 4qx1C 4qx3C 1dlcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.4 % |
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Crystal grow | Temperature: 303 K / Method: in vivo crystallization Details: Cry3A crystallized within the bacterial cell, IN VIVO CRYSTALLIZATION, temperature 303K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.457 Å |
Detector | Type: Cornell-SLAC Pixel Array Detector (CSPAD) / Detector: PIXEL / Date: Mar 11, 2013 |
Radiation | Monochromator: no monochromator, FEL beam with 20-30 eV bandwidth Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.457 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.9→2.99 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2.3 / % possible all: 39.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 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
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Displacement parameters | Biso mean: 38.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.317 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→52.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 36.2824 Å / Origin y: 42.4347 Å / Origin z: 46.5065 Å
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Refinement TLS group | Selection details: { A|* } |