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- PDB-4w8j: Structure of the full-length insecticidal protein Cry1Ac reveals ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4w8j | ||||||
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Title | Structure of the full-length insecticidal protein Cry1Ac reveals intriguing details of toxin packaging into in vivo formed crystals | ||||||
![]() | Pesticidal crystal protein cry1Ac | ||||||
![]() | TOXIN / insecticidal / pore forming / protoxin | ||||||
Function / homology | ![]() symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity / signaling receptor binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Evdokimov, A.G. / Moshiri, F. / Sturman, E.J. / Rydel, T.J. / Zheng, M. / Seale, J.W. / Franklin, S. | ||||||
![]() | ![]() Title: Structure of the full-length insecticidal protein Cry1Ac reveals intriguing details of toxin packaging into in vivo formed crystals. Authors: Evdokimov, A.G. / Moshiri, F. / Sturman, E.J. / Rydel, T.J. / Zheng, M. / Seale, J.W. / Franklin, 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 | ![]() | 217.7 KB | Display | ![]() |
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PDB format | ![]() | 168.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.1 KB | Display | ![]() |
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Full document | ![]() | 455.8 KB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 50.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: Protein | Mass: 133981.031 Da / Num. of mol.: 1 Mutation: C661S,C730S,C796S,C802S,C814S,C816S,C822S,C837S,C990S,C1025S,C1045S,C1063S,C1076S,C1125S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HD73_6004 / Plasmid: pCry1Ac Details (production host): sporulation promoter, chloramphenicol resistance Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.09 % / Description: tetragonal bipyramid |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.84 Details: 600 nL of 13 mg/mL protein in 20 mM ethanolamine buffer with 0.35 M NaCl was mixed with 600 nL of 700 mM sodium-potassium tartrate, 100 mM BIS-TRIS propane pH 7.84 and 120 nL of 9 mM n-decyl ...Details: 600 nL of 13 mg/mL protein in 20 mM ethanolamine buffer with 0.35 M NaCl was mixed with 600 nL of 700 mM sodium-potassium tartrate, 100 mM BIS-TRIS propane pH 7.84 and 120 nL of 9 mM n-decyl thiomaltoside, and the resulting 1.2 uL sitting drop was allowed to equili- brate against 80uL of the tartrate/BIS-TRIS propane reservoir solution at 19C. PH range: 7.8-7.9 |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2011 |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→87 Å / Num. obs: 26818 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.78→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: in house Resolution: 2.78→82.97 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.85 / SU B: 18.927 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.539 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.344 Å2
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Refinement step | Cycle: 1 / Resolution: 2.78→82.97 Å
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Refine LS restraints |
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