+Open data
-Basic information
Entry | Database: PDB / ID: 3gs1 | ||||||
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Title | An all-RNA Hairpin Ribozyme with mutation A38N1dA | ||||||
Components |
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Keywords | RNA / ribozyme / hairpin ribozyme / N1-deazaadenosine | ||||||
Function / homology | COBALT HEXAMMINE(III) / Chem-S9L / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / 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 | 3gs1.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gs1.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gs1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/3gs1 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/3gs1 | 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 Details: The sequence occurs naturally in the negative polarity strand of the tobacco rinsgpot virus satellite RNA |
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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 | #7: Chemical | ChemComp-S9L / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.42 % | ||||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 15, 2008 Details: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block. Rh-coat ed Si mirror for vertical focusing. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→30.19 Å / Num. obs: 8038 / % possible obs: 12 % / Observed criterion σ(I): 2.6 / Redundancy: 8.48 % / Biso Wilson estimate: 110.6 Å2 / Rmerge(I) obs: 0.502 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.85→3.03 Å / Redundancy: 8.48 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 23.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.85→25.39 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 43756.18 / 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: 81.9467 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→25.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→3.03 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 6
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