+Open data
-Basic information
Entry | Database: PDB / ID: 1wgj | ||||||
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Title | STRUCTURE OF INORGANIC PYROPHOSPHATASE | ||||||
Components | INORGANIC PYROPHOSPHATASE | ||||||
Keywords | HYDROLASE / PYROPHOSPHATE PHOSPHOHYDROLASE / MANGANESE | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Heikinheimo, P. / Lehtonen, J. / Goldman, A. | ||||||
Citation | Journal: Structure / Year: 1996 Title: The structural basis for pyrophosphatase catalysis. Authors: Heikinheimo, P. / Lehtonen, J. / Baykov, A. / Lahti, R. / Cooperman, B.S. / Goldman, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wgj.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wgj.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 1wgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/1wgj ftp://data.pdbj.org/pub/pdb/validation_reports/wg/1wgj | HTTPS FTP |
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-Related 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: 32225.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PRODUCT COMPLEX Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PPA1 / Plasmid: PKW9 / Gene (production host): PPA1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P00817, inorganic diphosphatase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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 % |
-Processing
Software |
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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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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