[English] 日本語
Yorodumi- PDB-1djz: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1djz | ||||||
---|---|---|---|---|---|---|---|
Title | PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH INOSITOL-4,5-BISPHOSPHATE | ||||||
Components | PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1 | ||||||
Keywords | LIPID DEGRADATION / PHOSPHORIC DIESTER HYDROLASE / HYDROLASE / TRANSDUCER / CALCIUM-BINDING / PHOSPHOLIPASE C / PHOSPHOINOSITIDE-SPECIFIC | ||||||
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 / phosphatidylinositol phosphate binding / phosphoinositide phospholipase C / positive regulation of norepinephrine secretion / phosphatidylinositol metabolic process / response to aluminum ion / 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 / phosphatidylinositol phosphate binding / phosphoinositide phospholipase C / positive regulation of norepinephrine secretion / phosphatidylinositol metabolic process / response to aluminum ion / phosphatidylinositol phospholipase C activity / phosphatidic acid binding / phospholipase C activity / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / phosphatidylinositol-mediated signaling / GTPase activating protein binding / labyrinthine layer blood vessel development / response to hyperoxia / lipid catabolic process / release of sequestered calcium ion into cytosol / response to organonitrogen compound / phosphatidylinositol-4,5-bisphosphate binding / regulation of cytosolic calcium ion concentration / 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 / SYNCHROTRON / Resolution: 2.95 Å | ||||||
Authors | Essen, L.-O. / Perisic, O. / Williams, R.L. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Structural mapping of the catalytic mechanism for a mammalian phosphoinositide-specific phospholipase C. Authors: Essen, L.O. / Perisic, O. / Katan, M. / Wu, Y. / Roberts, M.F. / Williams, R.L. #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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1djz.cif.gz | 232.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1djz.ent.gz | 185.7 KB | Display | PDB format |
PDBx/mmJSON format | 1djz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/1djz ftp://data.pdbj.org/pub/pdb/validation_reports/dj/1djz | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 INOSITOL-4,5-BISPHOSPHATE Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CDNA FRAGMENT / Plasmid: PGEX (PHARMACIA) / Gene (production host): CDNA FRAGMENT / Production host: Escherichia coli (E. coli) References: UniProt: P10688, phosphoinositide phospholipase C #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 70 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 12 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.988 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 30, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Num. obs: 55796 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.091 |
Reflection | *PLUS Highest resolution: 2.95 Å / Lowest resolution: 37 Å / Num. measured all: 326969 |
Reflection shell | *PLUS % possible obs: 92.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.326 |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.95→10 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→10 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.212 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|