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- PDB-3epl: Crystallographic snapshots of eukaryotic dimethylallyltransferase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3epl | ||||||
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Title | Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism | ||||||
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![]() | Transferase/RNA / Transferase / Alternative initiation / ATP-binding / Cytoplasm / Mitochondrion / Nucleotide-binding / Nucleus / tRNA processing / Transferase-RNA COMPLEX | ||||||
Function / homology | ![]() tRNA dimethylallyltransferase / tRNA dimethylallyltransferase activity / AMP dimethylallyltransferase activity / tRNA modification / tRNA binding / nucleolus / mitochondrion / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Huang, R.H. / Zhou, C. | ||||||
![]() | ![]() Title: Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism. Authors: Zhou, C. / Huang, R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.7 KB | Display | ![]() |
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PDB format | ![]() | 199.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.8 KB | Display | ![]() |
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Full document | ![]() | 566.4 KB | Display | |
Data in XML | ![]() | 44.2 KB | Display | |
Data in CIF | ![]() | 60.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48199.000 Da / Num. of mol.: 2 / Fragment: UNP residues 13-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MOD5 / Plasmid: pLM-1 / Production host: ![]() ![]() |
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-RNA chain , 2 types, 2 molecules EF
#2: RNA chain | Mass: 22294.254 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription with T7 RNA polymerase |
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#3: RNA chain | Mass: 22224.121 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 4 types, 130 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/DMA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MG / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.37 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / pH: 6.5 Details: Pentaerythritol propoxylate 426, pH 6.5, vapor diffusion, temperature 278K,, VAPOR DIFFUSION |
Components of the solutions | Name: Pentaerythritol propoxylate 426 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3.6→50 Å / Num. obs: 21517 |
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Processing
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Refinement | Resolution: 3.6→50 Å / Occupancy max: 1.01 / Occupancy min: 1 / FOM work R set: 0.823 / σ(F): 1495
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Solvent computation | Bsol: 60.132 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 220.56 Å2 / Biso mean: 135.038 Å2 / Biso min: 31.25 Å2
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Refinement step | Cycle: LAST / Resolution: 3.6→50 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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Xplor file |
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