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Yorodumi- PDB-3gs8: An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gs8 | ||||||
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Title | An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state 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: 2.85 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 | 3gs8.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gs8.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/3gs8 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/3gs8 | 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
-RNA chain , 4 types, 4 molecules ABCD
#1: RNA chain | Mass: 4358.636 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 3970.448 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: RNA chain | Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: RNA chain | Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 4 molecules
#5: Chemical | ChemComp-SO4 / |
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#6: Chemical | ChemComp-S9L / |
#7: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.31 Å3/Da / Density % sol: 71.47 % | ||||||||||||||||||||||||||||||||||||||||||||
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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 operated at 4.8 kW / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→38.5 Å / Num. obs: 8407 / Observed criterion σ(I): 12.2 / Redundancy: 3.81 % / Biso Wilson estimate: 1.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.2 / Num. unique all: 830 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.85→27.37 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 79272.77 / 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: 61.382 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 96.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→27.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.95 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
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Xplor file |
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