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Open data
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Basic information
Entry | Database: PDB / ID: 7e0v | |||||||||
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Title | GDPD from Pyrococcus furiosus DSM 3638 | |||||||||
![]() | Glycerophosphodiester phosphodiesterase | |||||||||
![]() | HYDROLASE / Glycerophosphate phosphodiesterase / Hydrolysis / glycerophosphorylcholine / lysophosphorylcholine | |||||||||
Function / homology | Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding / Glycerophosphodiester phosphodiesterase![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, Y.H. / Wang, J. / Wang, F.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Bomgl, a monoacylglycerol lipase from marine Bacillus Authors: Wang, Y.H. / Wang, J. / Wang, F.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 372.5 KB | Display | ![]() |
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PDB format | ![]() | 254.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
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Full document | ![]() | 438.2 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7e04C ![]() 7eoaC ![]() 4oecS S: Starting model for refinement C: citing same article ( |
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Similar 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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Components
#1: Protein | Mass: 29418.229 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.87 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M Hepes (pH 7.5), 25% w/v PEG3350, 0.2M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→66.44 Å / Num. obs: 68423 / % possible obs: 97.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.43 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.65→1.69 Å / Num. unique obs: 4817 / CC1/2: 0.654 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OEC Resolution: 1.65→66.44 Å / SU ML: 0.1458 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7406 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→66.44 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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