+Open data
-Basic information
Entry | Database: PDB / ID: 6prv | ||||||
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Title | 58nt RNA L11-binding domain from E. coli 23S rRNA | ||||||
Components | 23S rRNA | ||||||
Keywords | RNA / ribosome / 23S rRNA | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Conn, G.L. / Dunstan, M.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain. Authors: Welty, R. / Rau, M. / Pabit, S. / Dunstan, M.S. / Conn, G.L. / Pollack, L. / Hall, K.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6prv.cif.gz | 315.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6prv.ent.gz | 216.3 KB | Display | PDB format |
PDBx/mmJSON format | 6prv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/6prv ftp://data.pdbj.org/pub/pdb/validation_reports/pr/6prv | HTTPS FTP |
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-Related structure data
Related structure data | 1hc8S S: Starting model for refinement |
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Similar structure data |
-Links
-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: 18862.111 Da / Num. of mol.: 4 / Fragment: 58nt RNA L11-binding domain / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5-20 % PEG 4000, 0.6-1.2M NaCl and Sodium cacodylate (PH6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→40 Å / Num. obs: 22407 / % possible obs: 97.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 82.94 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.086 / Net I/σ(I): 12.92 |
Reflection shell | Resolution: 2.71→2.87 Å / Mean I/σ(I) obs: 4.9 / Num. unique obs: 3442 / CC1/2: 0.49 / Rrim(I) all: 2.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HC8 Resolution: 2.71→39.36 Å / SU ML: 0.4274 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.9446
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→39.36 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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