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Yorodumi- PDB-1mai: STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM PHOSPHOLIPASE C ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mai | ||||||
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Title | STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM PHOSPHOLIPASE C DELTA IN COMPLEX WITH INOSITOL TRISPHOSPHATE | ||||||
Components | PHOSPHOLIPASE C DELTA-1 | ||||||
Keywords | SIGNAL TRANSDUCTION PROTEIN / PLECKSTRIN / PHOSPHOLIPASE / INOSITOL TRISPHOSPHATE / HYDROLASE | ||||||
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 / MIR / Resolution: 1.9 Å | ||||||
Authors | Ferguson, K.M. / Lemmon, M.A. / Schlessinger, J. / Sigler, P.B. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1995 Title: Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain. Authors: Ferguson, K.M. / Lemmon, M.A. / Schlessinger, J. / Sigler, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mai.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mai.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/1mai ftp://data.pdbj.org/pub/pdb/validation_reports/ma/1mai | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15445.579 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH D-MYO-INOSITOL-1,4,5-TRISPHOSPHATE / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) References: UniProt: P10688, phosphoinositide phospholipase C |
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#2: Chemical | ChemComp-I3P / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
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: NSLS / Beamline: X25 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 11978 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Rsym value: 0.066 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.9→1.96 Å / Mean I/σ(I) obs: 3.22 / Rsym value: 0.38 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 27.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Rfactor all: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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