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Yorodumi- PDB-2d42: Crystal structure analysis of a non-toxic crystal protein from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d42 | ||||||
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Title | Crystal structure analysis of a non-toxic crystal protein from Bacillus thuringiensis | ||||||
Components | non-toxic crystal protein | ||||||
Keywords | TOXIN / parasporin / bacterial toxin / beta-pore-forming toxin / parasporal inclusion / hinge-bending motion | ||||||
Function / homology | Function and homology information Nuclear Transport Factor 2; Chain: A, - #380 / Proaerolysin, chain A, domain 3 / Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Proaerolysin; Chain A, domain 3 / Nuclear Transport Factor 2; Chain: A, / Beta Complex / Roll / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å | ||||||
Authors | Akiba, T. / Higuchi, K. / Mizuki, E. / Ekino, K. / Shin, T. / Ohba, M. / Kanai, R. / Harata, K. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Nontoxic crystal protein from Bacillus thuringiensis demonstrates a remarkable structural similarity to beta-pore-forming toxins Authors: Akiba, T. / Higuchi, K. / Mizuki, E. / Ekino, K. / Shin, T. / Ohba, M. / Kanai, R. / Harata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d42.cif.gz | 109.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d42.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 2d42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d42_validation.pdf.gz | 430.3 KB | Display | wwPDB validaton report |
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Full document | 2d42_full_validation.pdf.gz | 439.8 KB | Display | |
Data in XML | 2d42_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 2d42_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/2d42 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/2d42 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27565.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus thuringiensis (bacteria) / Strain: A1470 (formerly called 89-T-34-22) / References: UniProt: Q6L5X8*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 10%(v/v) 2-methyl-2,4-pentanediol, 50-100mM ammonium sulfate, 100mM sodium citrate, 1mM Na-EDTA, 1mM DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.07→47.67 Å / Num. obs: 41642 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.054 / Net I/σ(I): 32.8 | ||||||||||||||||||
Reflection shell | Resolution: 2.07→2.18 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 9.6 / Num. unique all: 6001 / Rsym value: 0.229 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.07→47.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2145829.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.4809 Å2 / ksol: 0.380301 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.07→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.2 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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