+Open data
-Basic information
Entry | Database: PDB / ID: 2isd | |||||||||
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Title | PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT | |||||||||
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 / 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 | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | |||||||||
Authors | Essen, L.-O. / Perisic, O. / Williams, R.L. | |||||||||
Citation | 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2isd.cif.gz | 240.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2isd.ent.gz | 191.8 KB | Display | PDB format |
PDBx/mmJSON format | 2isd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2isd_validation.pdf.gz | 396.5 KB | Display | wwPDB validaton report |
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Full document | 2isd_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 2isd_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 2isd_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/2isd ftp://data.pdbj.org/pub/pdb/validation_reports/is/2isd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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 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 | #3: Water | ChemComp-HOH / | |
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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: 4.63 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 / Details: pH 5.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / Method: vapor diffusion, hanging drop / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.86 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 2, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→53.1 Å / Num. obs: 103157 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.4→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.9 / % possible all: 95.3 |
Reflection | *PLUS Num. measured all: 420859 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→15 Å / Cross valid method: FREE R / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 3814 / Rfactor obs: 0.227 / Rfactor Rfree: 0.283 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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