+Open data
-Basic information
Entry | Database: PDB / ID: 5okn | ||||||
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Title | Crystal structure of human SHIP2 Phosphatase-C2 D607A mutant | ||||||
Components | Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 | ||||||
Keywords | HYDROLASE / SHIP2 / Phosphatase / C2 / phosphatidylinositol (3 / 4 / 5)-triphosphate | ||||||
Function / homology | Function and homology information negative regulation of insulin-like growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / ruffle assembly / regulation of actin filament organization / phosphatidylinositol dephosphorylation / endochondral ossification / phosphatidylinositol biosynthetic process / immune system process ...negative regulation of insulin-like growth factor receptor signaling pathway / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / inositol-polyphosphate 5-phosphatase activity / ruffle assembly / regulation of actin filament organization / phosphatidylinositol dephosphorylation / endochondral ossification / phosphatidylinositol biosynthetic process / immune system process / Synthesis of IP3 and IP4 in the cytosol / establishment of mitotic spindle orientation / Synthesis of PIPs at the plasma membrane / regulation of immune response / Interleukin receptor SHC signaling / SH2 domain binding / basal plasma membrane / post-embryonic development / filopodium / actin filament organization / response to insulin / SH3 domain binding / spindle pole / endocytosis / glucose metabolic process / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of protein localization / lamellipodium / actin binding / cell adhesion / nuclear speck / negative regulation of cell population proliferation / negative regulation of gene expression / Golgi apparatus / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Le Coq, J. / Lietha, D. | ||||||
Citation | Journal: Elife / Year: 2017 Title: Structural basis for interdomain communication in SHIP2 providing high phosphatase activity. Authors: Le Coq, J. / Camacho-Artacho, M. / Velazquez, J.V. / Santiveri, C.M. / Gallego, L.H. / Campos-Olivas, R. / Dolker, N. / Lietha, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5okn.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5okn.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5okn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/5okn ftp://data.pdbj.org/pub/pdb/validation_reports/ok/5okn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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8 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 52706.492 Da / Num. of mol.: 8 / Mutation: D607A Source method: isolated from a genetically manipulated source Details: The first two residues are from the expression vector in which the gene was cloned. Source: (gene. exp.) Homo sapiens (human) / Gene: INPPL1, SHIP2 / Plasmid: pOPINJ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2(DE3)pLysS References: UniProt: O15357, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase |
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-Non-polymers , 5 types, 320 molecules
#2: Chemical | ChemComp-B3P / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-MG / #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: 2.59 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Bis-Tris propane, pH 7.0, 0.4 M KSCN, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→49.17 Å / Num. obs: 119204 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.996 / Rpim(I) all: 0.055 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.7 / Rpim(I) all: 0.467 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→49.17 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / SU B: 25.312 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 1.121 / ESU R Free: 0.32 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.007 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→49.17 Å
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