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- PDB-1pyp: X-RAY DIFFRACTION STUDY OF INORGANIC PYROPHOSPHATASE FROM BAKER,S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pyp | ||||||
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Title | X-RAY DIFFRACTION STUDY OF INORGANIC PYROPHOSPHATASE FROM BAKER,S YEAST AT THE 3 ANGSTROMS RESOLUTION (RUSSIAN) | ||||||
![]() | INORGANIC PYROPHOSPHATASE | ||||||
![]() | ACID ANHYDRIDE 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. / Terzyan, S.S. / Vainshtein, B.K. | ||||||
![]() | Journal: Dokl.Akad.Nauk Sssr / Year: 1981 Title: X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at the 3 Angstroms Resolution (Russian) Authors: Arutiunian, E.G. / Terzian, S.S. / Voronova, A.A. / Kuranova, I.P. / Smirnova, E.A. / Vainstein, B.K. / Hohne, W.E. / Hansen, G. #1: ![]() Title: X-Ray Structural Investigation of Inorganic Pyrophosphatase from Baker,S Yeast at 3 Angstroms Resolution Authors: Arutyunyan, E.G. / Terzyan, S.S. / Voronova, A.A. / Kuranova, I.P. / Smirnova, E.A. / Vainshtein, B.K. / Hoehne, W.E. / Hansen, G. #2: ![]() Title: X-Ray Structural Investigation of Inorganic Pyrophosphatase of Baker Yeast. II. Phase Calculation and Structure Model at 6 Angstroms Resolution (Russian) Authors: Makhaldiani, V.V. / Smirnova, E.A. / Voronova, A.A. / Tovbis, A.B. / Kuranova, I.P. / Haratyunyan, E.G. / Vainshtein, B.K. / Bienwald, B. / Hansen, G. / Hoehne, W.E. #3: ![]() Title: X-Ray Structural Investigation of Inorganic Pyrophosphatase of Yeasts. II. Calculation of Phases and Structural Model at 6 Angstroms Resolution Authors: Makhaldianei, V.V. / Smirnova, E.A. / Voronova, A.A. / Tovbis, A.B. / Kuranova, I.P. / Arutyunyan, E.G. / Vainshtein, B.K. / Bienwald, B. / Hansen, G. / Hoehne, W.E. #4: ![]() Title: X-Ray Structural Investigation of Inorganic Pyrophosphatase of Baker Yeast. I. Growing of Crystals, Production of Derivatives and Determination of the Heavy Atom Positions in Them (Russian) Authors: Smirnova, E.A. / Makhaldiani, V.V. / Voronova, A.A. / Kuranova, I.P. / Harutyunyan, E.G. / Vainshtein, B.K. / Heitmann, P. / Hoehne, W.E. #5: ![]() Title: X-Ray Structural Investigation of Inorganic-Pyrophosphatase of Yeasts. I. Growth of Crystals, Formation of Derivatives, and Determination of the Positions of Their Heavy Atoms Authors: Smirnova, E.A. / Makhaldiani, V.V. / Voronova, A.A. / Kuranova, I.P. / Arutyunyan, E.G. / Vainshtein, B.K. / Heitmann, P. / Hoehne, W.E. #6: ![]() Title: X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at the 6 Angstroms Resolution (Russian) Authors: Makhaldiani, V.V. / Smirnova, E.A. / Voronova, A.A. / Kuranova, I.P. / Arutiunian, E.G. / Vainstein, B.K. / Hoehne, W.E. / Binwald, B. / Hansen, G. #7: ![]() Title: X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at a Resolution of 6 Angstroms Authors: Makhaldiani, V.V. / Smirnova, E.A. / Voronova, A.A. / Kuranova, I.P. / Arutyunyan, E.G. / Vainshtein, B.K. / Hoehne, W. / Binwald, B. / Hansen, G. #8: ![]() Title: Covalent Structural Analysis of Yeast Inorganic Pyrophosphatase Authors: Cohen, S.A. / Sterner, R. / Keim, P.S. / Heinrikson, R.L. | ||||||
History |
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Remark 700 | SHEET THE SIX-STRANDED BETA-SHEET *BAR* PRESENTED ON SHEET RECORDS BELOW IS ACTUALLY A FIVE- ...SHEET THE SIX-STRANDED BETA-SHEET *BAR* PRESENTED ON SHEET RECORDS BELOW IS ACTUALLY A FIVE-STRANDED BETA-BARREL. THIS IS DENOTED BY HAVING THE FIRST STRAND RECUR AS THE LAST. SHEET III IS A BIFURCATED SHEET. THE THIRD STRAND CONTAINS A BETA-TURN FROM RESIDUES 204-207. TO REPRESENT THIS, TWO SETS OF SHEET RECORDS (S3A, S3B) ARE PRESENTED BELOW, WHICH DIFFER ONLY IN THE THIRD STRAND. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 80.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 383.2 KB | Display | ![]() |
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Full document | ![]() | 592.3 KB | Display | |
Data in XML | ![]() | 43.3 KB | Display | |
Data in CIF | ![]() | 56.3 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.965279, -0.156618, -0.209069), Vector: Details | THE TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS BELOW WILL YIELD COORDINATES FOR THE OTHER MOLECULE IN THE ASYMMETRIC UNIT WHEN APPLIED TO THE COORDINATES IN THIS ENTRY. | |
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Components
#1: Protein | Mass: 32079.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00817, inorganic diphosphatase |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
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Processing
Refinement | Highest resolution: 3 Å Details: FOR PHASE DETERMINATION THREE ISOMORPHOUS HEAVY ATOM DERIVATIVES WERE USED. REFINEMENT OF THE PHASES WAS DONE USING MOLECULAR SYMMETRY. | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 3 Å
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