[English] 日本語
Yorodumi- PDB-2rci: High-resolution crystal structure of activated Cyt2Ba monomer fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rci | ||||||
---|---|---|---|---|---|---|---|
Title | High-resolution crystal structure of activated Cyt2Ba monomer from Bacillus thuringiensis subsp. israelensis | ||||||
Components | Type-2Ba cytolytic delta-endotoxin | ||||||
Keywords | TOXIN / alpha/beta architecture with beta-sheet surrounded by two alpha-helix layers / Structural Genomics / Israel Structural Proteomics Center / ISPC / Plasmid / Sporulation | ||||||
Function / homology | Function and homology information sporulation resulting in formation of a cellular spore / : / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus thuringiensis serovar israelensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dym, O. / Israel Structural Proteomics Center (ISPC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2rci.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2rci.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 2rci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rci_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2rci_full_validation.pdf.gz | 423.1 KB | Display | |
Data in XML | 2rci_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 2rci_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/2rci ftp://data.pdbj.org/pub/pdb/validation_reports/rc/2rci | HTTPS FTP |
-Related structure data
Related structure data | 1cbyS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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.) Bacillus thuringiensis serovar israelensis (bacteria) Strain: 4Q2, T301 / Gene: cyt2Ba1, cyt2Ba7, cytB / Production host: Escherichia coli (E. coli) / References: UniProt: Q45723 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.15 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.84 Å / Total num. of bins used: 20
|