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- PDB-6t19: Structure of mosquitocidal Cyt1A protoxin obtained by Serial Femt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t19 | |||||||||
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Title | Structure of mosquitocidal Cyt1A protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals soaked with DTT at pH 7 | |||||||||
![]() | Type-1Aa cytolytic delta-endotoxin | |||||||||
![]() | 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![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.6 KB | Display | ![]() |
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Full document | ![]() | 424 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t14SC ![]() 6t1aC ![]() 6t1cC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 Details: Structure solved from in vivo grown nanocrystals of Cyt1Aa soaked with 1mM DTT at pH 7 and room-temperature. Source: (gene. exp.) ![]() ![]() Gene: cyt1Aa, cytA Production host: ![]() ![]() Variant (production host): 4Q7 / References: UniProt: P0A382 |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.4 % / Description: bipyramidal crystals. |
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Crystal grow | Temperature: 300 K / Method: in cell 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: ![]() ![]() ![]() |
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: 1.83→50 Å / Num. obs: 18261 / % possible obs: 99.9 % / Redundancy: 160.5 % / CC1/2: 0.998 / R split: 0.074 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 1.83→1.85 Å / Redundancy: 30.8 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1003 / CC1/2: 0.164 / R split: 0.517 / % 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: 18766 / Frames total: 39547 / Lattices indexed: 18882 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6t14 Resolution: 1.85→14.838 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.197 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: 32.369 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→14.838 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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