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Yorodumi- PDB-3dvz: Crystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dvz | ||||||
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Title | Crystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA | ||||||
Components | Sarcin/Ricin Domain from E. Coli 23 S rRNA | ||||||
Keywords | RNA / Sarcin Ricin Loop | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å | ||||||
Authors | Olieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Briese, C. / Micura, R. / Dumas, P. / Ennifar, E. | ||||||
Citation | Journal: Rna / Year: 2009 Title: A fast selenium derivatization strategy for crystallization and phasing of RNA structures. Authors: Olieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Briese, C. / Micura, R. / Dumas, P. / Ennifar, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dvz.cif.gz | 45.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dvz.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/3dvz ftp://data.pdbj.org/pub/pdb/validation_reports/dv/3dvz | HTTPS FTP |
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-Related structure data
Related structure data | 3dw4C 3dw5C 3dw6C 3dw7C 1q9aS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 8744.255 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.29 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3.2 M (NH4)2SO4, 50 mM K-MOPS pH 7.0, 10 mM MgCl2, 10 mM MnCl2, vapor diffusion, hanging drop, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.85 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Highest resolution: 1 Å / Num. obs: 33970 / % possible obs: 96.6 % / Redundancy: 11.8 % / Biso Wilson estimate: 13.872 Å2 / Rsym value: 0.04 / Net I/σ(I): 28.37 |
Reflection shell | Resolution: 1→1.1 Å / Mean I/σ(I) obs: 3.9 / Num. measured obs: 59134 / Num. unique obs: 7559 / Rsym value: 0.506 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Starting model: 1q9a Resolution: 1→27.542 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.12 / σ(F): 2.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.988 Å2 / ksol: 0.456 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 39.14 Å2 / Biso mean: 15.434 Å2 / Biso min: 7.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1→27.542 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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