+Open data
-Basic information
Entry | Database: PDB / ID: 7y78 | ||||||
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Title | Crystal structure of Cry78Aa | ||||||
Components | Toxin | ||||||
Keywords | 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 / AMMONIUM ION / Toxin Function and homology information | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Cao, B.B. / Nie, Y.F. / Wang, N.C. / Guan, Z.Y. / Zhang, D.L. / Zhang, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Biol / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y78.cif.gz | 651.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y78.ent.gz | 455.1 KB | Display | PDB format |
PDBx/mmJSON format | 7y78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y78_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7y78_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7y78_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 7y78_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/7y78 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/7y78 | HTTPS FTP |
-Related structure data
Related structure data | 7y79C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39794.574 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3S6Q0Y2 #2: Chemical | ChemComp-NH4 / #3: Chemical | ChemComp-EDO / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.39 Å3/Da / Density % sol: 72.01 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, PEG3350, ammonium chloride / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 63102 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 67.16 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.043 / Rrim(I) all: 0.111 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4303 / CC1/2: 0.933 / Rpim(I) all: 0.292 / Rrim(I) all: 0.761 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→48.78 Å / SU ML: 0.4569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.0401 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 82.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→48.78 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: -36.5170765536 Å / Origin y: 2.8201423951 Å / Origin z: -38.9462525852 Å
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Refinement TLS group | Selection details: all |