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Open data
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Basic information
Entry | Database: PDB / ID: 7y79 | ||||||
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Title | Crystal structure of Cry78Aa | ||||||
![]() | Toxin | ||||||
![]() | TOXIN / Cry78Aa / plant hopper | ||||||
Function / homology | Insecticidal crystal toxin / Insecticidal Crystal Toxin, P42 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Ricin B, lectin domain / Ricin B-like lectins / toxin activity / Toxin![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, B.B. / Nie, Y.F. / Wang, N.C. / Guan, Z.Y. / Zhang, D.L. / Zhang, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of Cry78Aa from Bacillus thuringiensis provides insights into its insecticidal activity. Authors: Cao, B. / Nie, Y. / Guan, Z. / Chen, C. / Wang, N. / Wang, Z. / Shu, C. / Zhang, J. / Zhang, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.3 KB | Display | ![]() |
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PDB format | ![]() | 132.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7y78C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 24030.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.08 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, PEG3350, magnesium nitrate / PH range: 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→45 Å / Num. obs: 17763 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 41.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1742 / CC1/2: 0.84 / Rpim(I) all: 0.298 / Rrim(I) all: 0.782 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 50.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→28.01 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: 9.65991354125 Å / Origin y: 5.06173900144 Å / Origin z: 21.1081202049 Å
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Refinement TLS group | Selection details: all |