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Yorodumi- PDB-4oec: Crystal structure of glycerophosphodiester phosphodiesterase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oec | ||||||
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Title | Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1 | ||||||
Components | Glycerophosphoryl diester phosphodiesteraseGlycerophosphodiester phosphodiesterase | ||||||
Keywords | HYDROLASE / TIM Barrel | ||||||
Function / homology | Function and homology information phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Atsuta, Y. / You, D.J. / Takano, K. / Koga, Y. / Kanaya, S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of glycerophosphodiester phosphodiesterase from Thermococcus kodakarensis KOD1 Authors: Atsuta, Y. / You, D.J. / Takano, K. / Koga, Y. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oec.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oec.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 4oec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/4oec ftp://data.pdbj.org/pub/pdb/validation_reports/oe/4oec | HTTPS FTP |
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-Related structure data
Related structure data | 2otdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 28555.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1397 / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus References: UniProt: Q5JGZ3, glycerophosphodiester phosphodiesterase #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 43.28 % / Mosaicity: 0.507 ° / Mosaicity esd: 0.002 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30%(w/v) PEG4000, 0.2M Magnesium chloride hexahydrate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Jul 4, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 79998 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 23.493 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2otd Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2426 / WRfactor Rwork: 0.1901 / FOM work R set: 0.8283 / SU B: 3.673 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1734 / SU Rfree: 0.1639 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.6 Å2 / Biso mean: 30.063 Å2 / Biso min: 13.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.943 Å / Total num. of bins used: 20
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