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Yorodumi- PDB-4hne: Crystal structure of the catalytic domain of human type II alpha ... -
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-Basic information
Entry | Database: PDB / ID: 4hne | ||||||
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Title | Crystal structure of the catalytic domain of human type II alpha Phosphatidylinositol 4-kinase (PI4KIIalpha) in complex with ADP | ||||||
Components | Phosphatidylinositol 4-kinase type 2-alpha | ||||||
Keywords | TRANSFERASE / PI3K/PI4K kinase / lipid kinase / ATP Binding / palmitoylation / membrane anchoring | ||||||
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 / trans-Golgi network / presynaptic membrane / perikaryon / cytoplasmic vesicle / early endosome membrane / endosome / neuron projection / membrane raft / lysosomal membrane / phosphorylation / Golgi membrane / dendrite / neuronal cell body / magnesium ion binding / mitochondrion / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Zhou, Q. / Zhai, Y. / Zhang, K. / Chen, C. / Sun, F. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Molecular insights into the membrane-associated phosphatidylinositol 4-kinase II alpha. Authors: Zhou, Q. / Li, J. / Yu, H. / Zhai, Y. / Gao, Z. / Liu, Y. / Pang, X. / Zhang, L. / Schulten, K. / Sun, F. / Chen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hne.cif.gz | 297 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hne.ent.gz | 242.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/4hne ftp://data.pdbj.org/pub/pdb/validation_reports/hn/4hne | HTTPS FTP |
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-Related structure data
Related structure data | 4hndSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 43824.879 Da / Num. of mol.: 2 / Fragment: residues 78-453 / Mutation: C174S, C175S, C177S, C178S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: PI4K2A, PI4KIIA (AMINO ACIDS 78-453) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9BTU6, 1-phosphatidylinositol 4-kinase #2: Chemical | #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: 4.13 Å3/Da / Density % sol: 70.24 % |
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Crystal grow | Temperature: 289 K / pH: 5.8 Details: 0.1 M citric acid, 150 mM sodium chloride, 1 mM dithiothreitol, 20 mM magnesium chloride, 18% PEG400, 20 mM hexaethylene glycol monooctyl ether (C8E6), pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2012 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 30925 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Biso Wilson estimate: 80.7 Å2 / Rmerge(I) obs: 0.186 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 6 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 2.1 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HND Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / SU B: 29.442 / SU ML: 0.246 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.588 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.06 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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