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Yorodumi- PDB-1qat: 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE DELTA C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qat | ||||||
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Title | 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE DELTA COMPLEX WITH SAMARIUM (III) CHLORIDE | ||||||
Components | PHOSPHOLIPASE C DELTA-1 | ||||||
Keywords | HYDROLASE / LIPID DEGRADATION / TRANSDUCER / CALCIUM-BINDING | ||||||
Function / homology | Function and homology information Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / positive regulation of inositol trisphosphate biosynthetic process / phosphoinositide phospholipase C / positive regulation of norepinephrine secretion / phosphatidylinositol phosphate binding / response to aluminum ion / phosphatidylinositol metabolic process / phosphatidylinositol phospholipase C activity / phosphatidic acid binding ...Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / positive regulation of inositol trisphosphate biosynthetic process / phosphoinositide phospholipase C / positive regulation of norepinephrine secretion / phosphatidylinositol phosphate binding / response to aluminum ion / phosphatidylinositol metabolic process / phosphatidylinositol phospholipase C activity / phosphatidic acid binding / phospholipase C activity / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / GTPase activating protein binding / labyrinthine layer blood vessel development / phosphatidylinositol-mediated signaling / response to hyperoxia / lipid catabolic process / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / : / phosphatidylinositol-4,5-bisphosphate binding / mitochondrial membrane / phospholipid binding / response to peptide hormone / response to calcium ion / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell population proliferation / angiogenesis / G protein-coupled receptor signaling pathway / calcium ion binding / enzyme binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 3 Å | ||||||
Authors | Grobler, J.A. / Hurley, J.H. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: C2 domain conformational changes in phospholipase C-delta 1. Authors: Grobler, J.A. / Essen, L.O. / Williams, R.L. / Hurley, J.H. #1: Journal: Nature / Year: 1996 Title: Crystal Structure of a Mammalian Phosphoinositide-Specific Phospholipase C Delta Authors: Essen, L.O. / Perisic, O. / Cheung, R. / Katan, M. / Williams, R.L. #2: Journal: Protein Sci. / Year: 1996 Title: Expression, Characterization, and Crystallization of the Catalytic Core of Rat Phosphatidylinositide-Specific Phospholipase C Delta 1 Authors: Grobler, J.A. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qat.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qat.ent.gz | 164.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/1qat ftp://data.pdbj.org/pub/pdb/validation_reports/qa/1qat | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 70430.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PHOSHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C DELTA-1 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: SEED / Plasmid: PET / Production host: Escherichia coli (E. coli) References: UniProt: P10688, phosphoinositide phospholipase C #2: Chemical | ChemComp-SM / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.51 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: clusters formed by mixing - used as seeds in hanging drop pH: 6.5 Details: NEEDLE CLUSTERS WERE FORMED BY MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (22 MG/ML) WITH A WELL SOLUTION CONSISTING OF 0.1 M NA MES (PH 6.0), 0.2 M LICL, 20% GLYCEROL, AND 12-14 % PEG 8000. ...Details: NEEDLE CLUSTERS WERE FORMED BY MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (22 MG/ML) WITH A WELL SOLUTION CONSISTING OF 0.1 M NA MES (PH 6.0), 0.2 M LICL, 20% GLYCEROL, AND 12-14 % PEG 8000. FRAGMENTS OF THE NEEDLE CLUSTERS WERE USED TO SEED HANGING DROPS. THE WELL SOLUTION USED FOR THE SEEDING EXPERIMENTS WAS ADJUSTED TO 0.1M NA MES (PH 6.5), 0.2 M LICL, 20 % GLYCEROL, AND 6-8 % PEG 8000., clusters formed by mixing - used as seeds in hanging drops PH range: 6.0-6.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: used to seeding, Grobler, J.A., (1996) Protein Sci., 5, 680. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→60 Å / Num. obs: 24235 / % possible obs: 84.9 % / Observed criterion σ(I): -2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.248 / % possible all: 73.8 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: APO TRICLINIC PHOSPHOLIPASE C Resolution: 3→6 Å / Cross valid method: FREE R
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.09 Å /
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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