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Yorodumi- PDB-3gs5: An all-RNA hairpin ribozyme A38N1dA variant with a product mimic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gs5 | ||||||
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Title | An all-RNA hairpin ribozyme A38N1dA variant with a product mimic substrate strand | ||||||
Components |
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Keywords | RNA / hairpin ribozyme / RNA ribozyme / N1-deazaadenosine | ||||||
Function / homology | COBALT HEXAMMINE(III) / Chem-S9L / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.75 Å | ||||||
Authors | Spitale, R.C. / Volpini, R. / Heller, M.G. / Krucinska, J. / Cristalli, G. / Wedekind, J.E. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Identification of an imino group indispensable for cleavage by a small ribozyme. Authors: Spitale, R.C. / Volpini, R. / Heller, M.G. / Krucinska, J. / Cristalli, G. / Wedekind, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gs5.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gs5.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gs5_validation.pdf.gz | 423.6 KB | Display | wwPDB validaton report |
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Full document | 3gs5_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 3gs5_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 3gs5_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/3gs5 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/3gs5 | HTTPS FTP |
-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: 8067.876 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: RNA chain | Mass: 11571.971 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | ChemComp-S9L / | ||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.22 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20.5% (w/v) PEG 2K MME, 0.10 M Na-Cacodylate, 0.25 M Li2SO4, 2.5 mM Co(NH3)6Cl3, 2 mM spermidine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 8, 2008 / Details: VariMax optics (Rigaku) |
Radiation | Monochromator: 0.3 x 3 mm focusing cup / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→29.91 Å / Num. obs: 9256 / Observed criterion σ(I): 2.3 / Redundancy: 4.75 % / Biso Wilson estimate: 64.4 Å2 / Rmerge(I) obs: 0.488 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 4.75 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.3 / Num. unique all: 894 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.75→27.85 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 54013.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.6298 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 74.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→27.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.85 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
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Xplor file |
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