[English] 日本語
Yorodumi- PDB-8tfz: tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tfz | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | tRNA 2'-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with NAD | ||||||||||||||||||
Components | Probable RNA 2'-phosphotransferase | ||||||||||||||||||
Keywords | TRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / NAD | ||||||||||||||||||
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: 2.06 Å | ||||||||||||||||||
Authors | Jacewicz, A. / Dantuluri, S. / Shuman, S. | ||||||||||||||||||
Funding support | United States, 5items
| ||||||||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8tfz.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8tfz.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 8tfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/8tfz ftp://data.pdbj.org/pub/pdb/validation_reports/tf/8tfz | HTTPS FTP |
---|
-Related structure data
Related structure data | 8tfiSC 8tfxC 8tfyC 8tg3C 8tg4C 8tg6C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-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.) Pyrococcus horikoshii OT3 (archaea) / Gene: kptA, PH0160 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon Plus 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.66 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|