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Yorodumi- PDB-2ztb: Crystal structure of the parasporin-2 Bacillus thuringiensis toxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ztb | ||||||
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Title | Crystal structure of the parasporin-2 Bacillus thuringiensis toxin that recognizes cancer cells | ||||||
Components | Crystal protein | ||||||
Keywords | TOXIN / beta-hairpin | ||||||
Function / homology | Function and homology information Immunoglobulin-like - #3040 / Immunoglobulin-like - #4280 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A - #50 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacillus thuringiensis serovar dakota (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å | ||||||
Authors | Akiba, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structure of the parasporin-2 Bacillus thuringiensis toxin that recognizes cancer cells Authors: Akiba, T. / Abe, Y. / Kitada, S. / Kusaka, Y. / Ito, A. / Ichimatsu, T. / Katayama, H. / Akao, T. / Higuchi, K. / Mizuki, E. / Ohba, M. / Kanai, R. / Harata, K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization of parasporin-2, a Bacillus thuringiensis crystal protein with selective cytocidal activity against human cells Authors: Akiba, T. / Abe, Y. / Kitada, S. / Kusaka, Y. / Ito, A. / Ichimatsu, T. / Katayama, H. / Akao, T. / Higuchi, K. / Mizuki, E. / Ohba, M. / Kanai, R. / Harata, K. #2: Journal: J.Biol.Chem. / Year: 2004 Title: A Bacillus thuringiensis crystal protein with selective cytocidal action to human cells Authors: Ito, A. / Sasaguri, Y. / Kitada, S. / Kusaka, Y. / Kuwano, K. / Masutomi, K. / Mizuki, E. / Akao, T. / Ohba, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ztb.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ztb.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ztb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ztb_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
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Full document | 2ztb_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 2ztb_validation.xml.gz | 23 KB | Display | |
Data in CIF | 2ztb_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/2ztb ftp://data.pdbj.org/pub/pdb/validation_reports/zt/2ztb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27537.568 Da / Num. of mol.: 2 Fragment: the proteolytically activated form, UNP residues 52-302 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis serovar dakota (bacteria) Strain: A1547 / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7WZI1 |
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-Non-polymers , 5 types, 300 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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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: 5.85 Å3/Da / Density % sol: 78.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% (v/v) ethylene glycol, 8% (w/v) PEG 3350, 1mM TCEP, 50mM HEPES-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.3403, 1.3408, 1.3460 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2004 | ||||||||||||
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.38→29.75 Å / Num. obs: 50770 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 26.2 | ||||||||||||
Reflection shell | Resolution: 2.38→2.51 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 4.2 / Num. unique all: 7356 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.38→29.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.442 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.165 / Stereochemistry target values: Engh & Huber / 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: 58.421 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→29.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.441 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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