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Yorodumi- PDB-4phy: Functional conservation despite structural divergence in ligand-r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4phy | ||||||
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Title | Functional conservation despite structural divergence in ligand-responsive RNA switches | ||||||
Components |
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Keywords | RNA / Viral genome / internal ribosome entry site / translation | ||||||
Function / homology | ACETATE ION / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Seneca valley virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Boerneke, M.A. / Dibrov, S.M. / Hermann, T.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Functional conservation despite structural divergence in ligand-responsive RNA switches. Authors: Boerneke, M.A. / Dibrov, S.M. / Gu, J. / Wyles, D.L. / Hermann, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4phy.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4phy.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 4phy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/4phy ftp://data.pdbj.org/pub/pdb/validation_reports/ph/4phy | HTTPS FTP |
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-Related 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: 8206.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Seneca valley virus | ||
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#2: RNA chain | Mass: 6523.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Seneca valley virus | ||
#3: Chemical | #4: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: KCl, Magnesium Acetate, PEG 8K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→19.9 Å / Num. all: 3319 / Num. obs: 3167 / % possible obs: 88.15 % / Redundancy: 28 % / Net I/σ(I): 22.28 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 15.5 % / Mean I/σ(I) obs: 2.5 / % possible all: 56.4 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.375 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.991 Å2 / ksol: 0.243 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1→19.375 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→19.3749 Å
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Refinement TLS params. | Method: refined / Origin x: 15.5746 Å / Origin y: -25.3019 Å / Origin z: -13.2805 Å
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Refinement TLS group | Selection details: all |