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- PDB-2ik2: Yeast inorganic pyrophosphatase variant D115E with magnesium and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ik2 | ||||||
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Title | Yeast inorganic pyrophosphatase variant D115E with magnesium and phosphate | ||||||
![]() | Inorganic pyrophosphatase | ||||||
![]() | HYDROLASE / INORGANIC PYROPHOSPHATASE / STRUCTURE-FUNCTION / MUTAGENESIS | ||||||
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 | ![]() ![]() | ||||||
![]() | Oksanen, E. / Ahonen, A.K. / Tuominen, H. / Tuominen, V. / Lahti, R. / Goldman, A. / Heikinheimo, P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.4 KB | Display | ![]() |
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PDB format | ![]() | 108.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.8 KB | Display | ![]() |
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Full document | ![]() | 454.5 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 45.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ihpC ![]() 2ik0C ![]() 2ik1C ![]() 2ik4C ![]() 2ik6C ![]() 2ik7C ![]() 2ik9C ![]() 1hukS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: IPP1 / Plasmid: PKW9 / Production host: ![]() ![]() #2: Chemical | ChemComp-MG / #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: 2.57 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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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