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Yorodumi- PDB-4yc4: Crystal structure of phosphatidyl inositol 4-kinase II alpha in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yc4 | |||||||||
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Title | Crystal structure of phosphatidyl inositol 4-kinase II alpha in complex with nucleotide analog | |||||||||
Components | Phosphatidylinositol 4-kinase type 2-alpha,Lysozyme,Phosphatidylinositol 4-kinase type 2-alpha | |||||||||
Keywords | TRANSFERASE / Kinase / Complex / Inhibitor | |||||||||
Function / homology | Function and homology information growing cell tip / AP-3 adaptor complex binding / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / endosome organization / phosphatidylinositol biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane ...growing cell tip / AP-3 adaptor complex binding / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / endosome organization / phosphatidylinositol biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / viral release from host cell by cytolysis / peptidoglycan catabolic process / trans-Golgi network / cell wall macromolecule catabolic process / presynaptic membrane / lysozyme / lysozyme activity / perikaryon / cytoplasmic vesicle / early endosome membrane / host cell cytoplasm / endosome / neuron projection / defense response to bacterium / membrane raft / lysosomal membrane / phosphorylation / Golgi membrane / neuronal cell body / dendrite / magnesium ion binding / mitochondrion / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.58 Å | |||||||||
Authors | Klima, M. / Boura, E. | |||||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: The high-resolution crystal structure of phosphatidylinositol 4-kinase II beta and the crystal structure of phosphatidylinositol 4-kinase II alpha containing a nucleoside analogue provide a ...Title: The high-resolution crystal structure of phosphatidylinositol 4-kinase II beta and the crystal structure of phosphatidylinositol 4-kinase II alpha containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design. Authors: Klima, M. / Baumlova, A. / Chalupska, D. / Hrebabecky, H. / Dejmek, M. / Nencka, R. / Boura, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yc4.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yc4.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 4yc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/4yc4 ftp://data.pdbj.org/pub/pdb/validation_reports/yc/4yc4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 63240.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: PI4K2A, T4Tp126 / Plasmid: pRSFD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star References: UniProt: Q9BTU6, UniProt: D9IEF7, 1-phosphatidylinositol 4-kinase, lysozyme |
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#2: Chemical | ChemComp-M59 / [( |
#3: Chemical | ChemComp-ADP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 100 mM HEPES pH = 7.0, 10% w/v PEG 4000, 10% v/v 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→49.07 Å / Num. obs: 20124 / % possible obs: 95.77 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.0714 / Net I/σ(I): 15.98 |
Reflection shell | Resolution: 2.58→2.67 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.36 / % possible all: 74.15 |
-Processing
Software |
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Refinement | Resolution: 2.58→49.068 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→49.068 Å
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Refine LS restraints |
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LS refinement shell |
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