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Yorodumi- PDB-3awg: Crystal structure of Pten-like domain of Ci-VSP G356A mutant (248-576) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3awg | ||||||
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Title | Crystal structure of Pten-like domain of Ci-VSP G356A mutant (248-576) | ||||||
Components | Voltage-sensor containing phosphatase | ||||||
Keywords | HYDROLASE / MEMBRANE PROTEIN / PTDINS(3 / 4 / 5)P3 / PHOSPHATASE / ION CHANNEL | ||||||
Function / homology | Function and homology information regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol dephosphorylation / protein tyrosine phosphatase activity / cell projection / cell motility / monoatomic ion channel activity / negative regulation of cell population proliferation / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Ciona intestinalis (vase tunicate) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Matsuda, M. / Sakata, S. / Takeshita, K. / Suzuki, M. / Yamashita, E. / Okamura, Y. / Nakagawa, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structure of the cytoplasmic phosphatase and tensin homolog (PTEN)-like region of Ciona intestinalis voltage-sensing phosphatase provides insight into substrate specificity and redox ...Title: Crystal structure of the cytoplasmic phosphatase and tensin homolog (PTEN)-like region of Ciona intestinalis voltage-sensing phosphatase provides insight into substrate specificity and redox regulation of the phosphoinositide phosphatase activity Authors: Matsuda, M. / Takeshita, K. / Kurokawa, T. / Sakata, S. / Suzuki, M. / Yamashita, E. / Okamura, Y. / Nakagawa, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3awg.cif.gz | 198.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3awg.ent.gz | 158.7 KB | Display | PDB format |
PDBx/mmJSON format | 3awg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3awg_validation.pdf.gz | 464.2 KB | Display | wwPDB validaton report |
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Full document | 3awg_full_validation.pdf.gz | 474.5 KB | Display | |
Data in XML | 3awg_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 3awg_validation.cif.gz | 50.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/3awg ftp://data.pdbj.org/pub/pdb/validation_reports/aw/3awg | HTTPS FTP |
-Related structure data
Related structure data | 3aweC 3awfC 1d5rS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 38153.238 Da / Num. of mol.: 3 / Fragment: Pten-like region, residues 248-576 / Mutation: G356A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Plasmid: PET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codonplus-rilp References: UniProt: Q4W8A1, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: Chemical | ChemComp-SO4 / #3: 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: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.1M AMMONIUM SULFATE, 0.1M TRIS, 0.5M SODIUM FLUORIDE, 1.0M SODIUM MALONATE', pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Dec 7, 2008 / Details: HORIZONTAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. obs: 47922 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 18.51 |
Reflection shell | Resolution: 2.39→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.49 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D5R Resolution: 2.39→48.91 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 31.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→48.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.45 Å / Total num. of bins used: 20
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