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- PDB-2v7r: Crystal structure of a human tRNAGly microhelix at 1.2 Angstrom r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v7r | ||||||
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Title | Crystal structure of a human tRNAGly microhelix at 1.2 Angstrom resolution | ||||||
![]() | (HUMAN TRNAGLY MICROHELIX) x 2 | ||||||
![]() | RNA / TRNA / ACCEPTOR STEM / GLYCINE / MICROHELIX / IDENTITY / HYDRATION | ||||||
Function / homology | RNA![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Foerster, C. / Mankowska, M. / Fuerste, J.P. / Perbandt, M. / Betzel, C. / Erdmann, V.A. | ||||||
![]() | ![]() Title: Crystal Structure of a Human Trnagly Microhelix at 1.2 A Resolution. Authors: Foerster, C. / Mankowska, M. / Fuerste, J.P. / Perbandt, M. / Betzel, C. / Erdmann, V.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27.5 KB | Display | ![]() |
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PDB format | ![]() | 19.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.2 KB | Display | ![]() |
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Full document | ![]() | 383.4 KB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 4.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: RNA chain | Mass: 2253.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: RNA chain | Mass: 2179.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 59.4 % / Description: NONE |
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Crystal grow | Details: 40 MM SODIUM CACODYLATE, PH 6.0, 12 MM SPERMINE TETRA-HCL, 12 MM SODIUM CHLORIDE, 80 MM POTASSIUM CHLORIDE, 10% (V/V) MPD, EQUILIBRATED AGAINST 35% (V/V) MPD AT ROOM TEMPERATURE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8148 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 11547 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.24 / % possible all: 93.7 |
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Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→14.08 Å
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Refine LS restraints |
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