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- PDB-1t70: Crystal structure of a novel phosphatase from Deinococcus radiodurans -
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Open data
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Basic information
Entry | Database: PDB / ID: 1t70 | ||||||
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Title | Crystal structure of a novel phosphatase from Deinococcus radiodurans | ||||||
![]() | Phosphatase | ||||||
![]() | HYDROLASE / Crystal / phosphatase / X-ray crystallography / Structural Genomics / Berkeley Structural Genomics Center / BSGC / PSI / Protein Structure Initiative | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shin, D.H. / Wang, W. / Kim, R. / Yokota, H. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 396.3 KB | Display | ![]() |
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PDB format | ![]() | 321.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.7 KB | Display | ![]() |
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Full document | ![]() | 570.5 KB | Display | |
Data in XML | ![]() | 79.3 KB | Display | |
Data in CIF | ![]() | 105.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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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.) ![]() Strain: R1 / Plasmid: PSJS1244 / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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