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Yorodumi- PDB-2ybx: Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ybx | ||||||
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Title | Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha | ||||||
Components | PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE-2 ALPHA | ||||||
Keywords | TRANSFERASE / KINASE / SIGNALLING | ||||||
Function / homology | Function and homology information vesicle-mediated cholesterol transport / 1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / megakaryocyte development / PI5P Regulates TP53 Acetylation ...vesicle-mediated cholesterol transport / 1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / megakaryocyte development / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / autophagosome / photoreceptor outer segment / negative regulation of insulin receptor signaling pathway / photoreceptor inner segment / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / lysosome / protein homodimerization activity / nucleoplasm / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. ...Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. / Kotenyova, T. / Kouznetsova, E. / Nyman, T. / Persson, C. / Schuler, H. / Siponen, M.I. / Thorsell, A.G. / Wahlberg, E. / Weigelt, J. / Nordlund, P. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Phosphatidylinositol-5-Phosphate 4-Kinase Type-2 Alpha Authors: Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. / Kotenyova, T. / ...Authors: Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. / Kotenyova, T. / Kouznetsova, E. / Nyman, T. / Persson, C. / Schuler, H. / Siponen, M.I. / Thorsell, A.G. / Wahlberg, E. / Weigelt, J. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ybx.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ybx.ent.gz | 112.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ybx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/2ybx ftp://data.pdbj.org/pub/pdb/validation_reports/yb/2ybx | HTTPS FTP |
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-Related structure data
Related structure data | 1bo1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99988, 0.01034, -0.01175), Vector: |
-Components
#1: Protein | Mass: 45312.984 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-405 Source method: isolated from a genetically manipulated source Details: PHOSPHORYL-ASPARTATE INTERMEDIATE IN POSITION 359 / Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE References: UniProt: P48426, 1-phosphatidylinositol-5-phosphate 4-kinase #2: Chemical | ChemComp-PO4 / | #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: 2.51 Å3/Da / Density % sol: 56.5 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M MAGNESIUM FORMATE, 16% PEG3350, 2 MM BENZYL(1,3,5)TRIPHOSPHATE, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→28.47 Å / Num. obs: 28302 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 55.66 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.56→2.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.1 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BO1 Resolution: 2.56→28.37 Å / Cor.coef. Fo:Fc: 0.8973 / Cor.coef. Fo:Fc free: 0.8661 / SU R Cruickshank DPI: 0.428 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.401 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.267 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 49.11 Å2
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Refine analyze | Luzzati coordinate error obs: 0.314 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→28.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.56→2.66 Å / Total num. of bins used: 14
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