+Open data
-Basic information
Entry | Database: PDB / ID: 3awf | ||||||
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Title | Crystal structure of Pten-like domain of Ci-VSP (236-576) | ||||||
Components | Voltage-sensor containing phosphatase | ||||||
Keywords | HYDROLASE / MEMBRANE PROTEIN / PTDINS(3 / 4 / 5)P3 / PHOSPHATASE / ION CHANNEL | ||||||
Function / homology | Function and homology information phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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: 1.99 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 | 3awf.cif.gz | 208.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3awf.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 3awf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3awf_validation.pdf.gz | 472.4 KB | Display | wwPDB validaton report |
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Full document | 3awf_full_validation.pdf.gz | 480.6 KB | Display | |
Data in XML | 3awf_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 3awf_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/3awf ftp://data.pdbj.org/pub/pdb/validation_reports/aw/3awf | HTTPS FTP |
-Related structure data
Related structure data | 3aweC 3awgC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 39541.789 Da / Num. of mol.: 3 / Fragment: Pten-like region, residues 236-576 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: Ci-VSP / Plasmid: PET32 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) References: UniProt: Q4W8A1, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: 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: 2.51 Å3/Da / Density % sol: 50.91 % |
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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: 1.99→50 Å / Num. obs: 81701 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.621 |
Reflection shell | Resolution: 1.99→2.07 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.494 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D5R Resolution: 1.99→44.17 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.147 / 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: 28.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→44.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.04 Å / Total num. of bins used: 20
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