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Open data
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Basic information
Entry | Database: PDB / ID: 1ypp | ||||||
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Title | ACID ANHYDRIDE HYDROLASE | ||||||
![]() | INORGANIC PYROPHOSPHATASE | ||||||
![]() | HYDROLASE | ||||||
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 | ![]() ![]() | ||||||
![]() | Harutyunyan, E.H. / Kuranova, I.P. / Lamzin, V.S. / Dauter, Z. / Wilson, K.S. | ||||||
![]() | ![]() Title: X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate. Authors: Harutyunyan, E.H. / Kuranova, I.P. / Vainshtein, B.K. / Hohne, W.E. / Lamzin, V.S. / Dauter, Z. / Teplyakov, A.V. / Wilson, K.S. #1: ![]() Title: Structure of Inorganic Pyrophosphatase from E. Coli and its Complex with a Mn2+ Ion at 2.2 Angstroms Resolution Authors: Harutyunyan, E.H. / Oganessyan, V.Yu. / Oganessyan, N.N. / Terzyan, S.S. / Popov, A.N. / Rubinskiy, S.V. / Vainshtein, B.K. / Nazarova, T.I. / Kurilova, S.A. / Vorobyova, N.N. / Avaeva, S.M. #2: ![]() Title: New Crystal Forms of Escherichia Coli and Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatases Authors: Heikineimo, P. / Salminen, T. / Lahti, R. / Cooperman, B. / Goldman, A. #3: ![]() Title: Crystal Structure of Inorganic Pyrophosphatase from Thermus Thermophilus Authors: Teplyakov, A. / Obmolova, G. / Wilson, K.S. / Ishii, K. / Kaji, H. / Samejima, T. / Kuranova, I. #4: ![]() Title: The Structure of E.Coli Soluble Inorganic Pyrophosphatase at 2.7 A Resolution Authors: Kankare, J. / Neal, G.S. / Salminen, T. / Glumhoff, T. / Cooperman, B.S. / Lahti, R. / Goldman, A. #5: ![]() Title: Two Pathways of Pyrophosphate Hydrolysis and Synthesis by Yeast Inorganic Pyrophosphatase Authors: Baykov, A.A. / Shestakov, A.S. #6: ![]() Title: Crystal Structure of Mnpi Complex of Yeast Inorganic Pyrophosphatase at 2.35 Angstroms Resolution (Russian) Authors: Chirgadze, N.Yu. / Kuranova, I.P. / Nevskaya, N.A. / Teplyakov, A.V. / Wilson, K.S. / Strokopytov, B.N. / Harutyunyan, E.H. / Hohne, W.E. #7: ![]() Title: The Growing of Crystals of Inorganic Pyrophosphatase from Yeast with Metal Ions and Phosphate (Russian) Authors: Kuranova, I.P. / Smirnova, E.A. / Chirgadze, N.Yu. #8: ![]() Title: A Conformational Hypothesis of the Trans-Ligation of Metals which Activate Pyrophosphatase and Related Enzymes (Russian) Authors: Kuranova, I.P. / Sokolov, V.I. #9: ![]() Title: Inorganic Pyrophosphatase from Yeast at 3 A Resolution (Russian) Authors: Terzyan, S.S. / Voronova, A.A. / Smirnova, E.A. / Kuranova, I.P. / Nekrasov, Yu.V. / Harutyunyan, E.G. / Vainshtein, B.K. / Hohne, W. / Hansen, G. #10: ![]() Title: Investigations of the Metal Ion-Binding Sites of Yeast Inorganic Pyrophosphatase Authors: Knight, W.B. / Dunaway-Mariano, D. / Ransom, S.C. / Villafranca, J.J. #11: ![]() Title: The Mechanism of Action of Yeast Inorganic Pyrophosphatase Authors: Cooperman, B.S. #12: ![]() Title: Yeast Inorganic Pyrophosphatase: Studies on Metal Binding Authors: Baykov, A.A. / Avaeva, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.9 KB | Display | ![]() |
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PDB format | ![]() | 102.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419 KB | Display | ![]() |
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Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99734, -0.0405, -0.06061), Vector: Details | THE ASYMMETRIC UNIT CONTAINS A DIMER. THE TWO CHEMICALLY IDENTICAL SUBUNITS ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AXIS. ONLY 282 RESIDUES IN BOTH SUBUNITS ARE VISIBLE IN THE ELECTRON DENSITY. | |
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Components
#1: Protein | Mass: 32151.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #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: 2.69 Å3/Da / Density % sol: 54.19 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.2 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Redundancy: 3.4 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.095 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 21721 / % possible obs: 79 % |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.44 Å / % possible obs: 62 % / Rmerge(I) obs: 0.199 |
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Processing
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Refinement | Resolution: 2.4→10 Å / σ(F): 0 /
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Displacement parameters | Biso mean: 29.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |