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Yorodumi- PDB-5bzx: Crystal structure of human phosphatase PTEN treated with a bisper... -
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-Basic information
Entry | Database: PDB / ID: 5bzx | |||||||||
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Title | Crystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex | |||||||||
Components | Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN | |||||||||
Keywords | HYDROLASE / phosphatase / C2 domain / disulfide / oxidized / vanadate | |||||||||
Function / homology | Function and homology information inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity ...inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / phosphatidylinositol-3-phosphate phosphatase activity / central nervous system neuron axonogenesis / postsynaptic density assembly / neuron-neuron synaptic transmission / negative regulation of dendritic spine morphogenesis / presynaptic membrane assembly / Regulation of PTEN mRNA translation / synapse maturation / Negative regulation of the PI3K/AKT network / cellular response to electrical stimulus / negative regulation of cell cycle G1/S phase transition / negative regulation of axonogenesis / Transcriptional Regulation by MECP2 / myelin sheath adaxonal region / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / negative regulation of excitatory postsynaptic potential / negative regulation of organ growth / forebrain morphogenesis / negative regulation of focal adhesion assembly / Schmidt-Lanterman incisure / negative regulation of epithelial to mesenchymal transition / phosphatidylinositol dephosphorylation / anaphase-promoting complex binding / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / dentate gyrus development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / positive regulation of ubiquitin-dependent protein catabolic process / spindle assembly involved in female meiosis / phosphatidylinositol biosynthetic process / dendritic spine morphogenesis / negative regulation of cell size / brain morphogenesis / myosin phosphatase activity / protein serine/threonine phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / molecular function inhibitor activity / ubiquitin-specific protease binding / protein-serine/threonine phosphatase / regulation of neuron projection development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Synthesis of IP3 and IP4 in the cytosol / locomotor rhythm / negative regulation of vascular associated smooth muscle cell proliferation / social behavior / negative regulation of cellular senescence / phosphoprotein phosphatase activity / positive regulation of excitatory postsynaptic potential / Synthesis of PIPs at the plasma membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / multicellular organismal response to stress / localization / prepulse inhibition / negative regulation of peptidyl-serine phosphorylation / synapse assembly / Regulation of PTEN localization / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of cell migration / locomotory behavior / negative regulation of protein phosphorylation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / central nervous system development / protein tyrosine phosphatase activity / cell projection / PDZ domain binding / cell motility / TP53 Regulates Metabolic Genes / regulation of protein stability / cytoplasmic side of plasma membrane / PML body / Regulation of PTEN stability and activity / positive regulation of DNA-binding transcription factor activity / cell migration / Ovarian tumor domain proteases / negative regulation of neuron projection development / Downstream TCR signaling / heart development / dendritic spine / postsynaptic density / learning or memory / protein stabilization / Ub-specific processing proteases / neuron projection / apical plasma membrane / negative regulation of cell population proliferation / lipid binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | |||||||||
Authors | Lee, C.-U. / Bier, D. / Hennig, S. / Grossmann, T.N. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Redox Modulation of PTEN Phosphatase Activity by Hydrogen Peroxide and Bisperoxidovanadium Complexes. Authors: Lee, C.U. / Hahne, G. / Hanske, J. / Bange, T. / Bier, D. / Rademacher, C. / Hennig, S. / Grossmann, T.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bzx.cif.gz | 290.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bzx.ent.gz | 233.6 KB | Display | PDB format |
PDBx/mmJSON format | 5bzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/5bzx ftp://data.pdbj.org/pub/pdb/validation_reports/bz/5bzx | HTTPS FTP |
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-Related structure data
Related structure data | 5bugC 5bzzC 1d5rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37307.805 Da / Num. of mol.: 4 / Fragment: PTEN wt 7-353 delta 286-309 / Mutation: Deletion 286-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTEN, MMAC1, TEP1 / Plasmid: pFH1 Details (production host): Bacmid DNA derived from pFH1 transformed in DH10Bac E. coli Production host: Trichoplusia ni (cabbage looper) References: UniProt: P60484, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase #2: Chemical | #3: Chemical | #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: 3.15 Å3/Da / Density % sol: 60.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol / PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.77119 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.77119 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.5→46.293 Å / Num. obs: 65393 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.91 % / Biso Wilson estimate: 56.698 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.123 / Χ2: 0.949 / Net I/σ(I): 17.43 / Num. measured all: 843899 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1d5r Resolution: 2.5→46.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1852 / WRfactor Rwork: 0.1601 / FOM work R set: 0.8448 / SU B: 4.673 / SU ML: 0.111 / SU R Cruickshank DPI: 0.0763 / SU Rfree: 0.0467 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 146.99 Å2 / Biso mean: 59.842 Å2 / Biso min: 29.37 Å2
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Refinement step | Cycle: final / Resolution: 2.5→46.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.498→2.563 Å / Total num. of bins used: 20
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