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Open data
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Basic information
Entry | Database: PDB / ID: 1wgj | ||||||
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Title | STRUCTURE OF INORGANIC PYROPHOSPHATASE | ||||||
![]() | INORGANIC PYROPHOSPHATASE | ||||||
![]() | HYDROLASE / PYROPHOSPHATE PHOSPHOHYDROLASE / MANGANESE | ||||||
Function / homology | ![]() Cytosolic tRNA aminoacylation / Mitochondrial tRNA aminoacylation / Pyrophosphate hydrolysis / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Heikinheimo, P. / Lehtonen, J. / Goldman, A. | ||||||
![]() | ![]() Title: The structural basis for pyrophosphatase catalysis. Authors: Heikinheimo, P. / Lehtonen, J. / Baykov, A. / Lahti, R. / Cooperman, B.S. / Goldman, A. #1: ![]() Title: New Crystal Forms of E. Coli and S. Cerevisiae Soluble Inorganic Pyrophosphatases Authors: Heikinheimo, P. / Salminen, T. / Cooperman, B.S. / Lahti, R. / Goldman, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.6 KB | Display | ![]() |
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PDB format | ![]() | 101.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385 KB | Display | ![]() |
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Full document | ![]() | 389 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 32225.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PRODUCT COMPLEX Source: (gene. exp.) ![]() ![]() Gene: PPA1 / Plasmid: PKW9 / Gene (production host): PPA1 / Production host: ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Redundancy: 5.2 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.103 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. obs: 45565 / % possible obs: 89.2 % / Num. measured all: 236904 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.09 Å / % possible obs: 82.9 % |
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Processing
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Refinement | Resolution: 2→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 18.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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