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Open data
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Basic information
Entry | Database: PDB / ID: 5g37 | ||||||
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Title | MR structure of the binary mosquito larvicide BinAB at pH 5 | ||||||
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![]() | TOXIN / BINAB INSECTICIDAL TOXIN / PORE FORMING TOXIN / XFEL / SERIAL FEMTOSECOND CRYSTALLOGRAPHY / DE NOVO MIRAS PHASING / IN VIVO CRYSTALS | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 352.4 KB | Display | ![]() |
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PDB format | ![]() | 289.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.6 KB | Display | ![]() |
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Full document | ![]() | 441.3 KB | Display | |
Data in XML | ![]() | 35.9 KB | Display | |
Data in CIF | ![]() | 54.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5foySC ![]() 5fozC 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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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.) ![]() Production host: ![]() ![]() 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.) ![]() Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |