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Yorodumi- PDB-8t90: Crystal structure of Terrestrivirus Inositol pyrophosphatase kina... -
+Open data
-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 | ||||||
Components | Kinase | ||||||
Keywords | VIRAL PROTEIN / Virus / Kinase / inositol phosphate / soil | ||||||
Function / homology | Function and homology information inositol-1,4,5,6-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 | Terrestrivirus sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Zong, G. / Wang, H. / Shears, S.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Embo J. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t90.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t90.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 8t90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t90_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8t90_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8t90_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 8t90_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/8t90 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/8t90 | 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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Terrestrivirus sp. / Gene: Terrestrivirus9_15 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G4ZNY6 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→50 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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