[English] 日本語
![](img/lk-miru.gif)
- PDB-8tg5: tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in c... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8tg5 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with branched 2'-PO4 RNA | ||||||||||||||||||
![]() | Probable RNA 2'-phosphotransferase | ||||||||||||||||||
![]() | TRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / branched RNA / 2'-PO4 RNA | ||||||||||||||||||
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 | ![]()
| ||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 110.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 69.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8tfiC ![]() 8tfxC ![]() 8tfyC ![]() 8tfzC ![]() 8tg3C ![]() 8tg4C ![]() 8tg6C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20839.215 Da / Num. of mol.: 1 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 | ChemComp-9S2 / ( Mass: 1005.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H38N15O19P3 / Feature type: SUBJECT OF INVESTIGATION | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.85 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 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 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. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.34 Å / Num. obs: 15452 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 37.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.032 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.013 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1137 / CC1/2: 0.882 / Rpim(I) all: 0.314 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→42.64 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|