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Yorodumi- PDB-8tg3: tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tg3 | ||||||||||||||||||
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Title | tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-1" -phosphate | ||||||||||||||||||
Components | Probable RNA 2'-phosphotransferase | ||||||||||||||||||
Keywords | TRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / ADP-ribose-1"-phosphate / Aeropyrum pernix | ||||||||||||||||||
Function / homology | Function and homology information tRNA 2'-phosphotransferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / tRNA splicing, via endonucleolytic cleavage and ligation / NAD+-protein poly-ADP-ribosyltransferase activity Similarity search - Function | ||||||||||||||||||
Biological species | Aeropyrum pernix (archaea) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||||||||||||||
Authors | Jacewicz, A. / Dantuluri, S. / Shuman, S. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD. Authors: Jacewicz, A. / Dantuluri, S. / Shuman, S. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tg3.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tg3.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 8tg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/8tg3 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/8tg3 | HTTPS FTP |
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-Related structure data
Related structure data | 8tfiC 8tfxC 8tfyC 8tfzC 8tg4C 8tg5C 8tg6C 1wfxS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23382.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: kptA, APE_0204.1 / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon Plus References: UniProt: Q9YFP5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Non-polymers , 6 types, 187 molecules
#2: Chemical | ChemComp-HQG / [[( | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-K / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.59 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KNO3, pH 6.9, 20% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→55.88 Å / Num. obs: 29455 / % possible obs: 93.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 18.73 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.037 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 2 / Num. unique obs: 1392 / CC1/2: 0.809 / Rpim(I) all: 0.348 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WFX Resolution: 1.47→42.02 Å / SU ML: 0.1814 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3896 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→42.02 Å
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Refine LS restraints |
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LS refinement shell |
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