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Yorodumi- PDB-8tfx: tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tfx | ||||||||||||||||||
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Title | tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with 2',5'-ADP | ||||||||||||||||||
Components | Probable RNA 2'-phosphotransferase | ||||||||||||||||||
Keywords | TRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / 2' / 5'-ADP | ||||||||||||||||||
Function / homology | Function and homology information transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / tRNA splicing, via endonucleolytic cleavage and ligation / NAD+ ADP-ribosyltransferase activity Similarity search - Function | ||||||||||||||||||
Biological species | Pyrococcus horikoshii OT3 (archaea) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 8tfx.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tfx.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 8tfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/8tfx ftp://data.pdbj.org/pub/pdb/validation_reports/tf/8tfx | HTTPS FTP |
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-Related structure data
Related structure data | 8tfiSC 8tfyC 8tfzC 8tg3C 8tg4C 8tg6C S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20839.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: kptA, PH0160 / Plasmid: pET28b-His10Smt3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): (DE3) Codon Plus References: UniProt: O57899, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Non-polymers , 6 types, 131 molecules
#2: Chemical | ChemComp-A2P / | ||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Chemical | ChemComp-K / #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1-0.3 M Tris-Bicine (pH 8.3 or 8.5), 0.1 M amino acid additives mixture (0.02 M each of DL-glutamic acid monohydrate, DL-alanine, glycine, DL-lysine monohydrate and DL-serine), 16-29.6% ...Details: 0.1-0.3 M Tris-Bicine (pH 8.3 or 8.5), 0.1 M amino acid additives mixture (0.02 M each of DL-glutamic acid monohydrate, DL-alanine, glycine, DL-lysine monohydrate and DL-serine), 16-29.6% ethylene glycol, and 8-14.8% PEG-8000 PH range: 8.3-8.5 |
-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: Dec 18, 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: 1.7→44.63 Å / Num. obs: 24459 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 26.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.016 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1269 / CC1/2: 0.918 / Rpim(I) all: 0.223 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8TFI Resolution: 1.7→42 Å / SU ML: 0.2167 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3047 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: 32.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→42 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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