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- PDB-6cn2: Crystal structure of zebrafish Phosphatidylinositol-4-phosphate 5... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6cn2 | ||||||
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Title | Crystal structure of zebrafish Phosphatidylinositol-4-phosphate 5- kinase alpha isoform D236N with bound ATP/Ca2+ | ||||||
![]() | Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha | ||||||
![]() | TRANSFERASE / PIP5Ka / ATP / D236N | ||||||
Function / homology | ![]() Synthesis of PIPs at the plasma membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 1-phosphatidylinositol-4-phosphate 5-kinase / lipid kinase activity / 1-phosphatidylinositol-4-phosphate 5-kinase activity / phosphatidylinositol phosphate biosynthetic process / phosphorylation / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zeng, X. / Sui, D. / Hu, J. | ||||||
![]() | ![]() Title: Structural insights into lethal contractural syndrome type 3 (LCCS3) caused by a missense mutation of PIP5K gamma. Authors: Zeng, X. / Uyar, A. / Sui, D. / Donyapour, N. / Wu, D. / Dickson, A. / Hu, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.8 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cmwC ![]() 6cn3C ![]() 4tz7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44868.320 Da / Num. of mol.: 1 / Mutation: C-terminal fusion to HHHHHH, D236N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-ATP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.7 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10 mg/ml protein with 2 mM ATP and 10 mM MgCl2, mixed with 14% PEG8000, 100 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate and 20% glycerol |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→40 Å / Num. obs: 12117 / % possible obs: 100 % / Redundancy: 28.3 % / Biso Wilson estimate: 96.75 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.025 / Rrim(I) all: 0.121 / Χ2: 0.915 / Net I/σ(I): 6.3 / Num. measured all: 343402 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TZ7 Resolution: 3.102→36.065 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 228.71 Å2 / Biso mean: 90.5944 Å2 / Biso min: 39.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.102→36.065 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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