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Open data
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Basic information
Entry | Database: PDB / ID: 7e2b | |||||||||
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Title | GDPD mutant complex from Pyrococcus furiosus DSM 3638 | |||||||||
![]() | Glycerophosphodiester phosphodiesterase | |||||||||
![]() | HYDROLASE / Glycerophosphate phosphodiesterase / Hydrolysis / glycerophosphorylcholine / lysophosphorylcholine | |||||||||
Function / homology | ![]() phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, Y.H. / Wang, J. / Wang, F.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Observation of the GPC production during hydrolysis of LPC by GDPD D60A from Pyrococcus furiosus DSM 3638 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 | ![]() | 138 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 950.2 KB | Display | ![]() |
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Full document | ![]() | 944.8 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4oecS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29374.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PLM / |
#3: Chemical | ChemComp-CHT / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % |
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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: 1.85→70.12 Å / Num. obs: 26190 / % possible obs: 99.9 % / Observed criterion σ(I): 2.4 / Redundancy: 11.6 % / Biso Wilson estimate: 33.63 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.053 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.85→1.9 Å / Num. unique obs: 1875 / CC1/2: 0.534 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OEC Resolution: 1.85→20.83 Å / SU ML: 0.2344 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.8764 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: 41.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→20.83 Å
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Refine LS restraints |
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LS refinement shell |
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