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Yorodumi- PDB-2v7r: Crystal structure of a human tRNAGly microhelix at 1.2 Angstrom r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v7r | ||||||
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Title | Crystal structure of a human tRNAGly microhelix at 1.2 Angstrom resolution | ||||||
Components | (HUMAN TRNAGLY MICROHELIX) x 2 | ||||||
Keywords | RNA / TRNA / ACCEPTOR STEM / GLYCINE / MICROHELIX / IDENTITY / HYDRATION | ||||||
Function / homology | RNA Function and homology information | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Foerster, C. / Mankowska, M. / Fuerste, J.P. / Perbandt, M. / Betzel, C. / Erdmann, V.A. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v7r.cif.gz | 27.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7r.ent.gz | 19.6 KB | Display | PDB format |
PDBx/mmJSON format | 2v7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v7r_validation.pdf.gz | 383.2 KB | Display | wwPDB validaton report |
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Full document | 2v7r_full_validation.pdf.gz | 383.4 KB | Display | |
Data in XML | 2v7r_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 2v7r_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7r ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7r | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) HOMO SAPIENS (human) |
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#2: RNA chain | Mass: 2179.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8148 |
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 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→14.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.421 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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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