+Open data
-Basic information
Entry | Database: PDB / ID: 7e2a | |||||||||
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Title | GDPD mutant from Pyrococcus furiosus DSM 3638 | |||||||||
Components | Glycerophosphodiester phosphodiesterase | |||||||||
Keywords | 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 / Glycerophosphodiester phosphodiesterase Function and homology information | |||||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | |||||||||
Authors | Wang, Y.H. / Wang, J. / Wang, F.H. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Crystal structure of glycerophoshphodiester phospodiesterase D60A mutant from Pyrococcus furiosus DSM Authors: Wang, Y.H. / Wang, J. / Wang, F.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e2a.cif.gz | 131.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e2a.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 7e2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/7e2a ftp://data.pdbj.org/pub/pdb/validation_reports/e2/7e2a | HTTPS FTP |
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-Related structure data
Related structure data | 4oecS 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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Unit cell |
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-Components
#1: Protein | Mass: 29374.217 Da / Num. of mol.: 1 / Mutation: D60A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM 3638 / Gene: PF2003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZI9 |
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#2: 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: 2.5 Å3/Da / Density % sol: 50.72 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97921 Å |
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: 2.08→23.45 Å / Num. obs: 18312 / % possible obs: 99.9 % / Observed criterion σ(I): 2.7 / Redundancy: 12.9 % / Biso Wilson estimate: 39.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.08→2.13 Å / Num. unique obs: 1340 / CC1/2: 0.831 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OEC Resolution: 2.08→23.45 Å / SU ML: 0.2141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5643 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: 48.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→23.45 Å
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Refine LS restraints |
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LS refinement shell |
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