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Yorodumi- PDB-1vfg: Crystal structure of tRNA nucleotidyltransferase complexed with a... -
+Open data
-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 | ||||||
Components |
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Keywords | TRANSFERASE/RNA / TRANSFERASE / RNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / TRANSFERASE-RNA COMPLEX | ||||||
Function / homology | Function and homology information ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity / RNA 3'-end processing / tRNA processing / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Tomita, K. / Fukai, S. / Ishitani, R. / Ueda, T. / Takeuchi, N. / Vassylyev, D.G. / Nureki, O. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Nature / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vfg.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vfg.ent.gz | 150.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/1vfg ftp://data.pdbj.org/pub/pdb/validation_reports/vf/1vfg | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Aquifex aeolicus (bacteria) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O66728, polynucleotide adenylyltransferase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.000, 0.9793, 0.9795, 0.9843, 0.9743 | ||||||||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber 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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