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- PDB-1dji: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEX... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dji | ||||||
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Title | PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH CALCIUM | ||||||
![]() | PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1 | ||||||
![]() | LIPID DEGRADATION / PHOSPHORIC DIESTER HYDROLASE / HYDROLASE / TRANSDUCER / CALCIUM-BINDING / PHOSPHOLIPASE C / PHOSPHOINOSITIDE-SPECIFIC | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Essen, L.-O. / Perisic, O. / Williams, R.L. | ||||||
![]() | ![]() Title: A ternary metal binding site in the C2 domain of phosphoinositide-specific phospholipase C-delta1. Authors: Essen, L.O. / Perisic, O. / Lynch, D.E. / Katan, M. / Williams, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.2 KB | Display | ![]() |
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PDB format | ![]() | 196.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.5 KB | Display | ![]() |
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Full document | ![]() | 499.5 KB | Display | |
Data in XML | ![]() | 53.2 KB | Display | |
Data in CIF | ![]() | 77.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 70574.516 Da / Num. of mol.: 2 / Mutation: DELTA(1-132) DELETION VARIANT Source method: isolated from a genetically manipulated source Details: CATALYTICALLY-ACTIVE DELETION VARIANT THAT LACKS AN N-TERMINAL PH DOMAIN, COMPLEXED WITH CALCIUM Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P10688, phosphoinositide phospholipase C #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.65 Å3/Da / Density % sol: 73.56 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 12 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Essen, L.O., (1996) Nature, 380, 595. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 16, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Num. obs: 90470 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.073 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 34 Å / Num. measured all: 397693 |
Reflection shell | *PLUS % possible obs: 97.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.296 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.5→10 Å / Cross valid method: FREE R / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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