+Open data
-Basic information
Entry | Database: PDB / ID: 5g37 | ||||||
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Title | MR structure of the binary mosquito larvicide BinAB at pH 5 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g37.cif.gz | 352.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g37.ent.gz | 289.7 KB | Display | PDB format |
PDBx/mmJSON format | 5g37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g37_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
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Full document | 5g37_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 5g37_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 5g37_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g37 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g37 | HTTPS FTP |
-Related structure data
Related structure data | 5foySC 5fozC 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
#1: Protein | Mass: 41483.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LYSINIBACILLUS SPHAERICUS (bacteria) / Strain: 2362 / Plasmid: BTI4Q7-PPHSP-1 Production host: BACILLUS THURINGIENSIS SEROVAR ISRAELENSIS (bacteria) Strain (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 SEROVAR ISRAELENSIS (bacteria) Strain (production host): 4Q7 / References: UniProt: P10565 |
#3: Water | ChemComp-HOH / |
Sequence details | ONLY RESIDUES 3-366 ARE DEFINED IN THE ELECTRON DENSITY ONLY RESIDUES 29-448 ARE DEFINED IN THE ...ONLY RESIDUES 3-366 ARE DEFINED IN THE ELECTRON DENSITY ONLY RESIDUES 29-448 ARE DEFINED IN THE ELECTRON DENSITY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.4 % / Description: NONE |
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Crystal grow | pH: 5 Details: NATURALLY OCCURRING NANOCRYSTALS FORMED IN VIVO, pH 5 |
-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: 1.459 / Wavelength: 1.459 Å |
Detector | Type: CORNELL-SLAC / Detector: PIXEL / Date: Feb 13, 2015 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45 Å / Num. obs: 5495157 / % possible obs: 99.9 % / Observed criterion σ(I): 2.45 / Redundancy: 76.62 % / Biso Wilson estimate: 28.41 Å2 / CC1/2: 0.868 / Net I/σ(I): 6.34 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 8.61 % / Mean I/σ(I) obs: 2.46 / CC1/2: 0.28 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FOY Resolution: 2.5→24.643 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 28.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→24.643 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.8554 Å / Origin y: 37.721 Å / Origin z: 13.4776 Å
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Refinement TLS group | Selection details: ALL |