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- PDB-3eph: Crystallographic snapshots of eukaryotic dimethylallyltransferase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3eph | ||||||
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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 | ![]() | 259.3 KB | Display | ![]() |
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PDB format | ![]() | 202.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.6 KB | Display | ![]() |
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Full document | ![]() | 546.9 KB | Display | |
Data in XML | ![]() | 43.8 KB | Display | |
Data in CIF | ![]() | 61.7 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: chain A,B, using restrain) NCS domain segments: Dom-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 13 - 415 / Label seq-ID: 1 - 403
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Components
-Protein / RNA chain , 2 types, 4 molecules ABEF
#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, YOR274W / Plasmid: pLM-1 / Production host: ![]() ![]() #2: RNA chain | Mass: 22224.121 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription with T7 RNA polymerase |
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-Non-polymers , 4 types, 296 molecules ![](data/chem/img/ZN.gif)
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![](data/chem/img/PPV.gif)
![](data/chem/img/HOH.gif)
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#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.88 % |
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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: 2.95→50 Å / Num. obs: 40472 |
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Processing
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Refinement | Resolution: 2.95→50 Å / Occupancy max: 1.01 / Occupancy min: 1 / FOM work R set: 0.853 / σ(F): 3268
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Solvent computation | Bsol: 52.725 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200 Å2 / Biso mean: 91.406 Å2 / Biso min: 27.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms: 0.076 / Type: restrain / Weight: 100 | ||||||||||||||||||||||||||||
Xplor file |
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