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- PDB-7kio: Crystal structure of inositol polyphosphate 1-phosphatase (INPP1)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kio | ||||||||||||
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Title | Crystal structure of inositol polyphosphate 1-phosphatase (INPP1) D54A mutant | ||||||||||||
![]() | Inositol polyphosphate 1-phosphatase | ||||||||||||
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Function / homology | ![]() inositol-1,3,4-trisphosphate 1-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Xiong, J.-P. / Dollins, D.E. / Ren, Y. / York, J.D. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A structural basis for lithium and substrate binding of an inositide phosphatase. Authors: Dollins, D.E. / Xiong, J.P. / Endo-Streeter, S. / Anderson, D.E. / Bansal, V.S. / Ponder, J.W. / Ren, Y. / York, J.D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 57.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6wroC ![]() 6wrrC ![]() 6wryC ![]() 6x25C ![]() 7kirC ![]() 1inpS 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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Unit cell |
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Components
#1: Protein | Mass: 43932.922 Da / Num. of mol.: 1 / Mutation: D54A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P21327, ![]() | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.94 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium Citrate pH 4.3, 16-18% PEG6000, 5 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→28.93 Å / Num. obs: 14352 / % possible obs: 98.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.401 / Num. unique obs: 1311 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1INP Resolution: 2.4→28.93 Å / SU ML: 0.206 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.7232 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→28.93 Å
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Refine LS restraints |
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LS refinement shell |
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