+Open data
-Basic information
Entry | Database: PDB / ID: 5foy | ||||||
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Title | De novo structure of the binary mosquito larvicide BinAB at pH 7 | ||||||
Components |
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Keywords | TOXIN / BINAB INSECTICIDAL TOXIN / PORE FORMING TOXIN / XFEL / SERIAL FEMTOSECOND CRYSTALLOGRAPHY / DE NOVO MIRAS PHASING / IN VIVO CRYSTALS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LYSINIBACILLUS SPHAERICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MIRAS / Resolution: 2.25 Å | ||||||
Authors | Colletier, J.P. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Boutet, S. / Williams, G.J. / Messerschmidt, M. ...Colletier, J.P. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / DePonte, D.P. / Sierra, R.G. / Laksmono, H. / Koglin, J.E. / Hunter, M.S. / W Park, H. / Uervirojnangkoorn, M. / Bideshi, D.L. / Brunger, A.T. / Federici, B.A. / Sauter, N.K. / Eisenberg, D.S. | ||||||
Citation | Journal: Nature / Year: 2016 Title: De Novo Phasing with X-Ray Laser Reveals Mosquito Larvicide Binab Structure. Authors: Colletier, J. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Hice, R.H. / Coquelle, N. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / ...Authors: Colletier, J. / Sawaya, M.R. / Gingery, M. / Rodriguez, J.A. / Cascio, D. / Brewster, A.S. / Michels-Clark, T. / Hice, R.H. / Coquelle, N. / Boutet, S. / Williams, G.J. / Messerschmidt, M. / Deponte, D.P. / Sierra, R.G. / Laksmono, H. / Koglin, J.E. / Hunter, M.S. / Park, H. / Uervirojnangkoorn, M. / Bideshi, D.K. / Brunger, A.T. / Federici, B.A. / Sauter, N.K. / Eisenberg, D.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5foy.cif.gz | 338.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5foy.ent.gz | 286.7 KB | Display | PDB format |
PDBx/mmJSON format | 5foy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5foy_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 5foy_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 5foy_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 5foy_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/5foy ftp://data.pdbj.org/pub/pdb/validation_reports/fo/5foy | HTTPS FTP |
-Related 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: 41955.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LYSINIBACILLUS SPHAERICUS (bacteria) / Strain: 2362 / Description: NATURALLY OCCURRING NANO-CRYSTALS / Plasmid: BTI4Q7-PPHSP-1 Production host: BACILLUS THURINGIENSIS SUBSP. ISRAELENSIS (bacteria) Variant (production host): 4Q7 / References: UniProt: P06575 |
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#2: Protein | Mass: 51486.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LYSINIBACILLUS SPHAERICUS (bacteria) / Strain: 2362 / Description: NATURALLY OCCURRING NANO-CRYSTALS / Plasmid: BTI4Q7-PPHSP-1 Production host: BACILLUS THURINGIENSIS SUBSP. ISRAELENSIS (bacteria) Variant (production host): 4Q7 / References: UniProt: P10565 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.6 % / Description: NONE |
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Crystal grow | pH: 7 Details: NATURALLY OCCURRING NANOCRYSTALS FORMED IN VIVO, pH 7 |
-Data collection
Diffraction | Mean temperature: 287 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.212 / Wavelength: 1.212 Å |
Detector | Type: PIXEL ARRAY DETECTOR CSPAD / Detector: PIXEL / Date: Nov 9, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.212 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→43.5 Å / Num. obs: 6591964 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 65.9 % / Biso Wilson estimate: 35.82 Å2 / CC1/2: 0.968 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 5.7 / CC1/2: 0.262 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 2.25→39.687 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 18.79 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→39.687 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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