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Yorodumi- PDB-6wro: CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wro | ||||||||||||
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Title | CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM BUT NO LITHIUM AT 3 ANGSTROM RESOLUTION | ||||||||||||
Components | Inositol polyphosphate 1-phosphatase | ||||||||||||
Keywords | SIGNALING PROTEIN / inositol phosphate / neurological disease / Bipolar disorder / manic depressive illness / phosphatase / metal binding / cellular signaling | ||||||||||||
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 / FOURIER SYNTHESIS / Resolution: 3 Å | ||||||||||||
Authors | Dollins, D.E. / Endo-Streeter, S. / York, J.D. | ||||||||||||
Funding support | United States, 3items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wro.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wro.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/6wro ftp://data.pdbj.org/pub/pdb/validation_reports/wr/6wro | HTTPS FTP |
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-Related structure data
Related structure data | 6wrrC 6wryC 6x25C 7kioC 7kirC 1inpS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43976.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: INPP1 / Production host: Baculoviridae sp. (virus) References: UniProt: P21327, inositol-1,4-bisphosphate 1-phosphatase | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.39 % Description: Tetragonal shaped crystals amenable to diffraction studies were grown by the hanging drop vapor diffusion method on silanized glass covers slips at 20 C and grew with dimensions ...Description: Tetragonal shaped crystals amenable to diffraction studies were grown by the hanging drop vapor diffusion method on silanized glass covers slips at 20 C and grew with dimensions routinely exceeding 0.1 x 0.1 x 0.5mm |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: 10% PEG 8000, 80mM Bis-Tris, pH 5.25, 2mM Gd2(SO4)3 |
-Data collection
Diffraction | Mean temperature: 296 K / Ambient temp details: room temp / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å |
Detector | Type: UCSD MARK II / Detector: AREA DETECTOR / Date: Aug 10, 1994 / Details: supper |
Radiation | Monochromator: supper graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 3→8.3 Å / Num. obs: 12719 / % possible obs: 78.6 % / Redundancy: 1.3 % / Rsym value: 0.08 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 3→3.23 Å / Num. unique obs: 1000 / Rsym value: 0.159 / % possible all: 70 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1INP Resolution: 3→8.28 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.876 / SU B: 34.777 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.572 Å2
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Refinement step | Cycle: 1 / Resolution: 3→8.28 Å
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Refine LS restraints |
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