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Yorodumi- PDB-2ik2: Yeast inorganic pyrophosphatase variant D115E with magnesium and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ik2 | ||||||
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Title | Yeast inorganic pyrophosphatase variant D115E with magnesium and phosphate | ||||||
Components | Inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE / INORGANIC PYROPHOSPHATASE / STRUCTURE-FUNCTION / MUTAGENESIS | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Oksanen, E. / Ahonen, A.K. / Tuominen, H. / Tuominen, V. / Lahti, R. / Goldman, A. / Heikinheimo, P. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: A Complete Structural Description of the Catalytic Cycle of Yeast Pyrophosphatase. Authors: Oksanen, E. / Ahonen, A.K. / Tuominen, H. / Tuominen, V. / Lahti, R. / Goldman, A. / Heikinheimo, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ik2.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ik2.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ik2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/2ik2 ftp://data.pdbj.org/pub/pdb/validation_reports/ik/2ik2 | HTTPS FTP |
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-Related structure data
Related structure data | 2ihpC 2ik0C 2ik1C 2ik4C 2ik6C 2ik7C 2ik9C 1hukS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32239.398 Da / Num. of mol.: 2 / Mutation: D115E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: IPP1 / Plasmid: PKW9 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P00817, inorganic diphosphatase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PO4 / #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: 2.57 Å3/Da / Density % sol: 52.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6 Details: 16% MPD, 10 MM MGCL2, 1 MM PO4-, PH 6.0, VAPOR DIFFUSION, TEMPERATURE 277K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 2, 2004 / Details: MULTILAYER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 58354 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.344 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HUK Resolution: 1.8→19.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.637 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.533 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20 /
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