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- PDB-1vfg: Crystal structure of tRNA nucleotidyltransferase complexed with a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vfg | ||||||
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Title | Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog | ||||||
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![]() | TRANSFERASE/RNA / ![]() ![]() ![]() | ||||||
Function / homology | ![]() ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity / RNA 3'-end processing / tRNA processing / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tomita, K. / Fukai, S. / Ishitani, R. / Ueda, T. / Takeuchi, N. / Vassylyev, D.G. / Nureki, O. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structural basis for template-independent RNA polymerization. Authors: Tomita, K. / Fukai, S. / Ishitani, R. / Ueda, T. / Takeuchi, N. / Vassylyev, D.G. / Nureki, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.3 KB | Display | ![]() |
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PDB format | ![]() | 150.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 24155.350 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription with T7 RNA Polymerase in Thermotoga maritima #2: Protein | Mass: 45721.840 Da / Num. of mol.: 2 / Fragment: residues 1-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: O66728, ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70 % / Description: the file contains Friedel pairs | ||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, magnesium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 9, 2003 / Details: Si(111) | ||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. all: 39382 / Num. obs: 39382 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rsym value: 0.067 / Net I/σ(I): 22.4 | ||||||||||||||||||
Reflection shell | Resolution: 2.8→2.87 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.398 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: This crystal has a pseudo-merohedral perfect twinning in P2, which pretends P2(1)2(1)2. beta is 90 degree since Depositors processed the data with P2(1)2(1)2, and expanded them to the P2 ...Details: This crystal has a pseudo-merohedral perfect twinning in P2, which pretends P2(1)2(1)2. beta is 90 degree since Depositors processed the data with P2(1)2(1)2, and expanded them to the P2 space group. The file contains Friedel pairs.
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Displacement parameters | Biso mean: 87.8 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å
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