[English] 日本語
Yorodumi- PDB-7kir: Crystal structure of inositol polyphosphate 1-phosphatase (INPP1)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kir | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of inositol polyphosphate 1-phosphatase (INPP1) D54A mutant in complex with inositol (1,4)-bisphosphate | ||||||||||||
Components | Inositol polyphosphate 1-phosphatase | ||||||||||||
Keywords | HYDROLASE | ||||||||||||
Function / homology | Function and homology information inositol-1,3,4-trisphosphate 1-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol-1,4-bisphosphate 1-phosphatase / inositol-1,4-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Dollins, D.E. / Xiong, J.-P. / Ren, Y. / York, J.D. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7kir.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7kir.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 7kir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kir_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7kir_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7kir_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 7kir_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/7kir ftp://data.pdbj.org/pub/pdb/validation_reports/ki/7kir | HTTPS FTP |
-Related structure data
Related structure data | 6wroC 6wrrC 6wryC 6x25C 7kioC 1inpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43932.922 Da / Num. of mol.: 1 / Mutation: D54A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: INPP1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P21327, inositol-1,4-bisphosphate 1-phosphatase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-2IP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.84 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: Crystals were first grown in 0.1M sodium citrate pH 4.3, 16-18% PEG6K, 5 mM CaCl2. Then crystals were soaked with inositol (1,4)-bisphosphate for 1-3 hours |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.5418 Å |
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: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→35.3 Å / Num. obs: 10601 / % possible obs: 92.8 % / Biso Wilson estimate: 31.65 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.099 / Num. unique obs: 929 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1INP Resolution: 2.6→35.25 Å / SU ML: 0.321 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 24.9723 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→35.25 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|