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Yorodumi- PDB-6t1a: Structure of mosquitocidal Cyt1Aa protoxin obtained by Serial Fem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t1a | |||||||||
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Title | Structure of mosquitocidal Cyt1Aa protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals at pH 10 | |||||||||
Components | Type-1Aa cytolytic delta-endotoxin | |||||||||
Keywords | TOXIN / Mosquitocidal toxin / in vivo grown nanocrystals | |||||||||
Function / homology | Delta-endotoxin CytB / Delta-endotoxin CytB-like superfamily / Bacillus thuringiensis toxin / sporulation resulting in formation of a cellular spore / toxin activity / extracellular region / Type-1Aa cytolytic delta-endotoxin Function and homology information | |||||||||
Biological species | Bacillus thuringiensis subsp. israelensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Tetreau, G. / Banneville, A.S. / Andreeva, E. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Young, I.D. / Boutet, S. / Coquelle, N. / Cascio, D. ...Tetreau, G. / Banneville, A.S. / Andreeva, E. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Young, I.D. / Boutet, S. / Coquelle, N. / Cascio, D. / Sawaya, M.R. / Sauter, N.K. / Colletier, J.P. | |||||||||
Funding support | France, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade. Authors: Tetreau, G. / Banneville, A.S. / Andreeva, E.A. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Teulon, J.M. / Young, I.D. / Burke, N. / Grunewald, T.A. / Beaudouin, J. / Snigireva, I. / ...Authors: Tetreau, G. / Banneville, A.S. / Andreeva, E.A. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Teulon, J.M. / Young, I.D. / Burke, N. / Grunewald, T.A. / Beaudouin, J. / Snigireva, I. / Fernandez-Luna, M.T. / Burt, A. / Park, H.W. / Signor, L. / Bafna, J.A. / Sadir, R. / Fenel, D. / Boeri-Erba, E. / Bacia, M. / Zala, N. / Laporte, F. / Despres, L. / Weik, M. / Boutet, S. / Rosenthal, M. / Coquelle, N. / Burghammer, M. / Cascio, D. / Sawaya, M.R. / Winterhalter, M. / Gratton, E. / Gutsche, I. / Federici, B. / Pellequer, J.L. / Sauter, N.K. / Colletier, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t1a.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t1a.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6t1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/6t1a ftp://data.pdbj.org/pub/pdb/validation_reports/t1/6t1a | HTTPS FTP |
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-Related structure data
Related structure data | 6t14SC 6t19C 6t1cC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27354.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis subsp. israelensis (bacteria) Gene: cyt1Aa, cytA Production host: Bacillus thuringiensis serovar israelensis (bacteria) Variant (production host): 4Q7 / References: UniProt: P0A382 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.62 % / Description: bipyramidal crystals. |
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Crystal grow | Temperature: 300 K / Method: in cell / pH: 10.3 Details: In cell crystallization by recombinant expression in a Bacillus thuringiensis serovar israelensis strain devoid of its pBt plasmid. |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.28 Å |
Detector | Type: CS-PAD CXI-2 / Detector: PIXEL / Date: Nov 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 18439 / % possible obs: 99.9 % / Redundancy: 165.4 % / CC1/2: 0.998 / R split: 0.07 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 33.6 % / Num. unique obs: 910 / CC1/2: 0.073 / R split: 0.495 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 1.7 µm2 / Pulse duration: 40 fsec. / Pulse energy: 1000 µJ / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Description: MESH |
Serial crystallography data reduction | Frames indexed: 19924 / Frames total: 45117 / Lattices indexed: 20052 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6t14 Resolution: 1.85→26.824 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.163 / Cross valid method: FREE R-VALUE / ESU R: 0.236 / ESU R Free: 0.199 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.123 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→26.824 Å
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Refine LS restraints |
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LS refinement shell |
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