+Open data
-Basic information
Entry | Database: PDB / ID: 1bo1 | ||||||
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Title | PHOSPHATIDYLINOSITOL PHOSPHATE KINASE TYPE II BETA | ||||||
Components | PROTEIN (PHOSPHATIDYLINOSITOL PHOSPHATE KINASE IIBETA) | ||||||
Keywords | TRANSFERASE / LIPID SIGNALING | ||||||
Function / homology | Function and homology information 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 / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...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 / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / autophagosome / negative regulation of insulin receptor signaling pathway / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell surface receptor signaling pathway / endoplasmic reticulum membrane / GTP binding / protein homodimerization activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å | ||||||
Authors | Rao, V.D. / Misra, S. / Boronenkov, I.V. / Anderson, R.A. / Hurley, J.H. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Structure of type IIbeta phosphatidylinositol phosphate kinase: a protein kinase fold flattened for interfacial phosphorylation. Authors: Rao, V.D. / Misra, S. / Boronenkov, I.V. / Anderson, R.A. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bo1.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bo1.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bo1_validation.pdf.gz | 379.5 KB | Display | wwPDB validaton report |
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Full document | 1bo1_full_validation.pdf.gz | 406.3 KB | Display | |
Data in XML | 1bo1_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1bo1_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/1bo1 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/1bo1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: (-0.996792, 0.067419, -0.043137), Vector: |
-Components
#1: Protein | Mass: 47447.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: HUMAN ENZYME CLONED INTO E.COLI. / Plasmid: PET28B / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) References: UniProt: P78356, 1-phosphatidylinositol-4-phosphate 5-kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 100MM SODIUM CITRATE PH5.6 200MM MAGNESIUM ACETATE 100MM LITHIUM ACETATE 16% PEG (4000) | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 21621 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rsym value: 0.052 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.325 / % possible all: 98.3 |
Reflection | *PLUS Num. measured all: 297963 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 98.3 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 3→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 48.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.12 Å / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 5 % |