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Yorodumi- PDB-7yw3: Crystal structure of tRNA 2'-phosphotransferase from Homo sapiens -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yw3 | ||||||
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Title | Crystal structure of tRNA 2'-phosphotransferase from Homo sapiens | ||||||
Components | tRNA 2'-phosphotransferase 1 | ||||||
Keywords | TRANSFERASE / tRNA 2'-phosphotransferase | ||||||
Function / homology | Function and homology information 2'-phosphotransferase / tRNA 2'-phosphotransferase activity / tRNA splicing, via endonucleolytic cleavage and ligation / regulation of protein kinase activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Yang, X.Y. / Liu, X.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation. Authors: Yang, X. / Wang, J. / Li, S. / Li, X. / Gong, J. / Yan, Z. / Zhou, H. / Wu, C. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yw3.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yw3.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 7yw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/7yw3 ftp://data.pdbj.org/pub/pdb/validation_reports/yw/7yw3 | HTTPS FTP |
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-Related structure data
Related structure data | 7yw2C 7yw4C 6e3aS 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
#1: Protein | Mass: 27781.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRPT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86TN4, 2'-phosphotransferase |
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#2: Chemical | ChemComp-HQG / [[( |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 0.1M Tris pH 8.0 28 % PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→25.38 Å / Num. obs: 8284 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 38.57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.05 / Rrim(I) all: 0.127 / Net I/σ(I): 11.8 / Num. measured all: 53150 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6e3a Resolution: 2.5→25.38 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 114.02 Å2 / Biso mean: 48.2627 Å2 / Biso min: 27.32 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→25.38 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 99 %
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