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Yorodumi- PDB-1t70: Crystal structure of a novel phosphatase from Deinococcus radiodurans -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t70 | ||||||
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Title | Crystal structure of a novel phosphatase from Deinococcus radiodurans | ||||||
Components | Phosphatase | ||||||
Keywords | HYDROLASE / Crystal / phosphatase / X-ray crystallography / Structural Genomics / Berkeley Structural Genomics Center / BSGC / PSI / Protein Structure Initiative | ||||||
Function / homology | Function and homology information phosphoenolpyruvate phosphatase / phosphoenolpyruvate phosphatase activity / 2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Shin, D.H. / Wang, W. / Kim, R. / Yokota, H. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Structural and enzymatic characterization of DR1281: A calcineurin-like phosphoesterase from Deinococcus radiodurans. Authors: Shin, D.H. / Proudfoot, M. / Lim, H.J. / Choi, I.K. / Yokota, H. / Yakunin, A.F. / Kim, R. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t70.cif.gz | 396.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t70.ent.gz | 321.8 KB | Display | PDB format |
PDBx/mmJSON format | 1t70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/1t70 ftp://data.pdbj.org/pub/pdb/validation_reports/t7/1t70 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 27971.512 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: phosphatase activity aginst p-nitrophenylphosphate Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: R1 / Plasmid: PSJS1244 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RUV0 #2: 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: 2.67 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: n-hexyl beta-D glucose, PEG 4000, CAPS, Lithium Sulfate, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 16, 2003 / Details: Monochromator |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→111.8 Å / Num. all: 205986 / Num. obs: 194039 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.9 Å2 |
Reflection shell | Resolution: 2.3→2.34 Å / % possible all: 58.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→19.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 113819.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.5226 Å2 / ksol: 0.319787 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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