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Yorodumi- PDB-8prk: THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8prk | ||||||
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Title | THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC IMPLICATIONS | ||||||
Components | PROTEIN (INORGANIC PYROPHOSPHATASE) | ||||||
Keywords | HYDROLASE / ENZYME MECHANISM / IORGANIC PYROPHOSPHATASE / MUTANT STRUCTURES / 2-METAL ION MECHANISM | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Tuominen, V. / Heikinheimo, P. / Kajander, T. / Torkkel, T. / Hyytia, T. / Kapyla, J. / Lahti, R. / Cooperman, B.S. / Goldman, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: The R78K and D117E active-site variants of Saccharomyces cerevisiae soluble inorganic pyrophosphatase: structural studies and mechanistic implications. Authors: Tuominen, V. / Heikinheimo, P. / Kajander, T. / Torkkel, T. / Hyytia, T. / Kapyla, J. / Lahti, R. / Cooperman, B.S. / Goldman, A. #1: 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. #2: Journal: Eur.J.Biochem. / Year: 1996 Title: A Site-Directed Mutagenesis Study of Saccharomyces Cerevisiae Pyrophosphatase Functional Conservation of the Active Site of Soluble Inorganic Pyrophosphatases Authors: Heikinheimo, P. / Pohjanjoki, P. / Helminen, A. / Tasanen, M. / Cooperman, B.S. / Goldman, A. / Baykov, A. / Lahti, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8prk.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8prk.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 8prk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8prk ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8prk | HTTPS FTP |
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-Related structure data
Related structure data | 117eC 1wgjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.799085, 0.601106, 0.011616), Vector: |
-Components
#1: Protein | Mass: 32328.555 Da / Num. of mol.: 2 / Mutation: R78K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Cellular location: CYTOPLASM / Gene: PPA1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / Keywords: PRODUCT COMPLEX / References: UniProt: P00817, inorganic diphosphatase #2: Chemical | ChemComp-MN / #3: Chemical | #4: 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: 2.71 Å3/Da / Density % sol: 54.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 17-19 % MPD 25 MM MES, PH 6.0 1 MM MNCL2 0.5 MM NA2HPO4 10 MG/ML PROTEIN | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.891 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.891 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 54387 / % possible obs: 89.3 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.85→1.88 Å / % possible all: 92.5 |
Reflection | *PLUS Rmerge(I) obs: 0.062 / Num. measured all: 524728 |
Reflection shell | *PLUS % possible obs: 92.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WGJ Resolution: 1.85→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 12 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.88 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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