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- PDB-8t90: Crystal structure of Terrestrivirus Inositol pyrophosphatase kina... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t90 | ||||||
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Title | Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and myo-(3OH)IP5 | ||||||
![]() | Kinase | ||||||
![]() | VIRAL PROTEIN / Virus / Kinase / inositol phosphate / soil | ||||||
Function / homology | ![]() inositol tetrakisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate biosynthetic process / phosphatidylinositol phosphate biosynthetic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zong, G. / Wang, H. / Shears, S.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus. Authors: Zong, G. / Desfougeres, Y. / Portela-Torres, P. / Kwon, Y.U. / Saiardi, A. / Shears, S.B. / Wang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.6 KB | Display | ![]() |
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PDB format | ![]() | 43.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t8uC ![]() 8t8vC ![]() 8t8wC ![]() 8t8xC ![]() 8t8yC ![]() 8t8zC ![]() 8t91C ![]() 8t92C ![]() 8t93C ![]() 8t95C ![]() 8t96C ![]() 8t97C ![]() 8t98C ![]() 8t99C ![]() 8tf9C ![]() 8tfaC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Components
#1: Protein | Mass: 28688.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ZNZ / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% PEG8000, 100mM HEPES pH 7.0, 10mM NaH2PO4, 10% Ethylene Glycol, 5mM ADP and 10mM MgCl2, then soaked in 25% PEG8000, 100mM HEPES pH 7.0, 20% Ethylene Glycol with 5mM myo-(3OH)-IP5, 5mM ADP and 10mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 15669 / % possible obs: 99.9 % / Redundancy: 12.2 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.078 / Χ2: 0.931 / Net I/σ(I): 11 / Num. measured all: 191597 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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