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Open data
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Basic information
Entry | Database: PDB / ID: 1e9g | ||||||
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Title | STRUCTURE OF INORGANIC PYROPHOSPHATASE | ||||||
![]() | INORGANIC PYROPHOSPHATASE | ||||||
![]() | HYDROLASE / PYROPHOSPHATE PHOSPHOHYDROLASE / MANGANESE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Heikinheimo, P. / Tuominen, V. / Ahonen, A.-K. / Teplyakov, A. / Cooperman, B.S. / Baykov, A.A. / Lahti, R. / Goldman, A. | ||||||
![]() | ![]() Title: Toward a Quantum-Mechanical Description of Metal-Assisted Phosphoryl Transfer in Pyrophosphatase Authors: Heikinheimo, P. / Tuominen, V. / Ahonen, A.-K. / Teplyakov, A. / Cooperman, B.S. / Baykov, A.A. / Lahti, R. / Goldman, A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 446.5 KB | Display | ![]() |
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PDB format | ![]() | 360.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.3 KB | Display | ![]() |
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Full document | ![]() | 441.3 KB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 54.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e6aC ![]() 1wgjS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.7976, 0.6031, 0.015), Vector: |
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Components
#1: Protein | Mass: 32225.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PRODUCT COMPLEX Source: (gene. exp.) ![]() ![]() Cellular location: CYTOPLASM / Gene: PPA1 / Plasmid: PKW9 / Gene (production host): PPA1 / Production host: ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | Compound details | IN PRESENCE OF DIVALENT METAL CATION CATALYSES THE REACTION: PYROPHOSPHATE + H(2)O = 2 ...IN PRESENCE OF DIVALENT METAL CATION CATALYSES THE REACTION: PYROPHOSPH | Sequence details | 1WGJ A SWS P00817 283 - 286 NOT IN ATOMS LIST 1WGJ B SWS P00817 283 - 286 NOT IN ATOMS LIST | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 54.73 % Description: TWO MERGED DATA SETS: THE FIRST COLLECTED SEP-1996, WAVLENGTH 0.891 A, RESOLUTION RANGE 8-1.5 A AND THE SECOND COLLECTED 1997, WAVELENGTH 0.901 A, RESOLUTION RANGE 2.5-1.15 A | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Heikinheimo, P., (1996) Structure, 4, 1491. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.891 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→8 Å / Num. obs: 212495 / % possible obs: 85.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.95 |
Reflection shell | Resolution: 1.15→1.17 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 75.5 |
Reflection shell | *PLUS % possible obs: 75.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WGJ Resolution: 1.15→8 Å / Num. parameters: 51975 / Num. restraintsaints: 60843 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4.7% THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 42 / Occupancy sum hydrogen: 4448 / Occupancy sum non hydrogen: 5562.12 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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