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- PDB-2rci: High-resolution crystal structure of activated Cyt2Ba monomer fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2rci | ||||||
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Title | High-resolution crystal structure of activated Cyt2Ba monomer from Bacillus thuringiensis subsp. israelensis | ||||||
![]() | Type-2Ba cytolytic delta-endotoxin | ||||||
![]() | TOXIN / alpha/beta architecture with beta-sheet surrounded by two alpha-helix layers / Structural Genomics / Israel Structural Proteomics Center / ISPC / Plasmid / Sporulation | ||||||
Function / homology | ![]() sporulation resulting in formation of a cellular spore / : / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dym, O. / Israel Structural Proteomics Center (ISPC) | ||||||
![]() | ![]() Title: High-resolution crystal structure of activated Cyt2Ba monomer from Bacillus thuringiensis subsp. israelensis. Authors: Cohen, S. / Dym, O. / Albeck, S. / Ben-Dov, E. / Cahan, R. / Firer, M. / Zaritsky, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.6 KB | Display | ![]() |
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PDB format | ![]() | 37.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1cbyS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22973.137 Da / Num. of mol.: 1 / Fragment: Residues 35-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 4Q2, T301 / Gene: cyt2Ba1, cyt2Ba7, cytB / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.15 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7 Details: 1M Na/K Tartrate, 0.1M Tris-HCl pH 7.0, 0.2M Li2SO4, MICROBATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 16805 / Num. obs: 16805 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.075 / Rsym value: 0.103 / Net I/σ(I): 16.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1CBY Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.409 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.127 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.831 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.84 Å / Total num. of bins used: 20
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