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Yorodumi- PDB-2x6h: THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x6h | ||||||
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Title | THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 | ||||||
Components | PHOSPHOTIDYLINOSITOL 3 KINASE 59F | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information positive regulation of nurse cell apoptotic process / omegasome / Synthesis of PIPs at the Golgi membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / larval midgut cell programmed cell death / Macroautophagy / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II ...positive regulation of nurse cell apoptotic process / omegasome / Synthesis of PIPs at the Golgi membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / larval midgut cell programmed cell death / Macroautophagy / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / dsRNA transport / epithelial structure maintenance / protein targeting to lysosome / phagophore assembly site / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / regulation of early endosome to late endosome transport / 1-phosphatidylinositol-3-kinase activity / establishment or maintenance of cell polarity / neuron remodeling / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / autophagosome membrane / autophagosome assembly / cellular response to starvation / regulation of autophagy / autophagy / endocytosis / peroxisome / early endosome / endosome / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Miller, S. / Tavshanjian, B. / Oleksy, A. / Perisic, O. / Houseman, B.T. / Shokat, K.M. / Williams, R.L. | ||||||
Citation | Journal: Science / Year: 2010 Title: Shaping Development of Autophagy Inhibitors with the Structure of the Lipid Kinase Vps34. Authors: Miller, S. / Tavshanjian, B. / Oleksy, A. / Perisic, O. / Houseman, B.T. / Shokat, K.M. / Williams, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x6h.cif.gz | 229.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x6h.ent.gz | 183 KB | Display | PDB format |
PDBx/mmJSON format | 2x6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x6h_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 2x6h_full_validation.pdf.gz | 518.4 KB | Display | |
Data in XML | 2x6h_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 2x6h_validation.cif.gz | 61.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/2x6h ftp://data.pdbj.org/pub/pdb/validation_reports/x6/2x6h | HTTPS FTP |
-Related structure data
Related structure data | 2x6fC 2x6iC 2x6jC 2x6kC 1e8xS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.006037, -0.1229, -0.9924), Vector: |
-Components
#1: Protein | Mass: 78765.469 Da / Num. of mol.: 2 / Fragment: HELICAL DOMAIN, KINASE DOMAIN, RESIDUES 258-949 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 RIPL References: UniProt: Q9W1M7, phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, phosphatidylinositol-4-phosphate 3-kinase #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 4.16 Å3/Da / Density % sol: 70.22 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLISED IN 0.88M AMMONIUM SULPHATE, 100MM DI-POTASSIUM HYDROGEN PHOSPHATE AND 100MM DI-SODIUM HYDROGEN PHOSPHATE (TITRATED TO PH 7.5 WITH ORTHOPHOSPHORIC ACID). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→72.36 Å / Num. obs: 44562 / % possible obs: 95.8 % / Observed criterion σ(I): 0.9 / Redundancy: 3.39 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.77 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 2.86 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 0.86 / % possible all: 84.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E8X Resolution: 2.9→72.36 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.89 / SU B: 37.781 / SU ML: 0.315 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.831 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→72.36 Å
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Refine LS restraints |
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