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Yorodumi- PDB-6pmp: Crystal structure of a fragment of rat phospholipase Cepsilon EF3-RA1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pmp | ||||||||||||
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Title | Crystal structure of a fragment of rat phospholipase Cepsilon EF3-RA1 | ||||||||||||
Components | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 | ||||||||||||
Keywords | SIGNALING PROTEIN / phospholipase / lipase / TIM barrel / Ras-association domain | ||||||||||||
Function / homology | Function and homology information Synthesis of IP3 and IP4 in the cytosol / : / regulation of Ras protein signal transduction / phosphoinositide phospholipase C / diacylglycerol biosynthetic process / phosphatidylinositol phospholipase C activity / regulation of G protein-coupled receptor signaling pathway / phospholipase C activity / glomerulus development / regulation of protein kinase activity ...Synthesis of IP3 and IP4 in the cytosol / : / regulation of Ras protein signal transduction / phosphoinositide phospholipase C / diacylglycerol biosynthetic process / phosphatidylinositol phospholipase C activity / regulation of G protein-coupled receptor signaling pathway / phospholipase C activity / glomerulus development / regulation of protein kinase activity / phosphatidylinositol-mediated signaling / positive regulation of lamellipodium assembly / lipid catabolic process / guanyl-nucleotide exchange factor activity / epidermal growth factor receptor signaling pathway / small GTPase binding / lamellipodium / phospholipase C-activating G protein-coupled receptor signaling pathway / Ras protein signal transduction / G protein-coupled receptor signaling pathway / Golgi membrane / enzyme binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||||||||
Authors | Rugema, N.Y. / Lyon, A.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Commun Biol / Year: 2020 Title: Structure of phospholipase C epsilon reveals an integrated RA1 domain and previously unidentified regulatory elements. Authors: Rugema, N.Y. / Garland-Kuntz, E.E. / Sieng, M. / Muralidharan, K. / Van Camp, M.M. / O'Neill, H. / Mbongo, W. / Selvia, A.F. / Marti, A.T. / Everly, A. / McKenzie, E. / Lyon, A.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pmp.cif.gz | 999.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pmp.ent.gz | 816.3 KB | Display | PDB format |
PDBx/mmJSON format | 6pmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pmp_validation.pdf.gz | 250.2 KB | Display | wwPDB validaton report |
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Full document | 6pmp_full_validation.pdf.gz | 250.1 KB | Display | |
Data in XML | 6pmp_validation.xml.gz | 1 KB | Display | |
Data in CIF | 6pmp_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/6pmp ftp://data.pdbj.org/pub/pdb/validation_reports/pm/6pmp | HTTPS FTP |
-Related structure data
Related structure data | 3ohm S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 92569.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plce1, Plce / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q99P84, phosphoinositide phospholipase C #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.21 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 285.15 K / Method: vapor diffusion, hanging drop / Details: 6.25% PEG 4000, 100 mM MES pH 6.00, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.73→136.72 Å / Num. obs: 84933 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.171 / Rrim(I) all: 0.319 / Net I/σ(I): 5.1 / Num. measured all: 288747 / Scaling rejects: 500 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OHM 3ohm Resolution: 2.73→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.9 / SU B: 51.094 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R: 2.22 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.286 Å2
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Refinement step | Cycle: 1 / Resolution: 2.73→20 Å
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Refine LS restraints |
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