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Yorodumi- PDB-6wrr: CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wrr | ||||||||||||
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Title | CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AND LITHIUM AT 2.5 ANGSTROM RESOLUTION | ||||||||||||
Components | Inositol polyphosphate 1-phosphatase | ||||||||||||
Keywords | SIGNALING PROTEIN / inositol phosphate / neurological disease / Bipolar disorder / manic depressive illness / phosphatase | ||||||||||||
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: 2.5 Å | ||||||||||||
Authors | Dollins, D.R. / 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 | 6wrr.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wrr.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/6wrr ftp://data.pdbj.org/pub/pdb/validation_reports/wr/6wrr | HTTPS FTP |
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-Related structure data
Related structure data | 6wroC 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. Gd3+, a competitive inhibitor of Mg2+, has a useful anomalous absorption edge at the CuK wavelength and therefore was used in the co-crystallization or soaking conditions. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 13% PEG8000, 200mM Li2SO4 and 100mM Tris, pH 6.3. Upon reaching maximum size after ~5 days, a Gd3+ heavy atom derivative was prepared by adding 0.5uL of 17.5mM Gd2(SO4)3 in reservoir ...Details: 13% PEG8000, 200mM Li2SO4 and 100mM Tris, pH 6.3. Upon reaching maximum size after ~5 days, a Gd3+ heavy atom derivative was prepared by adding 0.5uL of 17.5mM Gd2(SO4)3 in reservoir solution to 3uL hanging drops (2.5mM final Gd3+) containing native crystals for 48 hours |
-Data collection
Diffraction | Mean temperature: 296 K / 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: Jul 10, 1992 |
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: 2.5→15.45 Å / Num. obs: 26197 / % possible obs: 96 % / Redundancy: 3.4 % / Rsym value: 0.051 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.5→2.69 Å / Num. unique obs: 2250 / Rsym value: 0.172 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1INP Resolution: 2.5→15.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.952 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.616 / ESU R Free: 0.248 / 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: 32.228 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→15.45 Å
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