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- PDB-8tfz: tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tfz | ||||||||||||||||||
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Title | tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with NAD | ||||||||||||||||||
![]() | Probable RNA 2'-phosphotransferase | ||||||||||||||||||
![]() | TRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / NAD | ||||||||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Jacewicz, A. / Dantuluri, S. / Shuman, S. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.8 KB | Display | ![]() |
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PDB format | ![]() | 129.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1022.9 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tfiSC ![]() 8tfxC ![]() 8tfyC ![]() 8tg3C ![]() 8tg4C ![]() 8tg5C ![]() 8tg6C S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 20678.955 Da / Num. of mol.: 2 / Mutation: R14A, M113G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O57899, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.66 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-Bicine (pH 8.5), 0.12 M divalent cations mixture (0.06 M each of magnesium chloride hexahydrate and calcium chloride dihydrate), 12.5 % MPD, 12.5% PEG-1000, and 12.5% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 3, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 20494 / % possible obs: 95.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 33.88 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.052 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.06→2.1 Å / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2 / Num. unique obs: 1027 / CC1/2: 0.471 / Rpim(I) all: 0.358 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8TFI Resolution: 2.06→37.63 Å / SU ML: 0.346 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.672 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: 37.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→37.63 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 |
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