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- PDB-2oue: Crystal structure of a junctionless all-RNA hairpin ribozyme at 2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oue | |||||||||
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Title | Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution | |||||||||
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![]() | RNA / hairpin ribozyme / all-RNA / mutation / low salt / S-turn / E-loop / ribose zipper / catalytic RNA | |||||||||
Function / homology | COBALT HEXAMMINE(III) / RNA / RNA (> 10)![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wedekind, J.E. | |||||||||
![]() | ![]() Title: Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer. Authors: Salter, J. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.2 KB | Display | ![]() |
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PDB format | ![]() | 33.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zftC ![]() 1zfvC ![]() 1zfxC ![]() 2bcyC ![]() 2bczC ![]() 2fgpC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-RNA chain , 4 types, 4 molecules ABCD
#1: RNA chain | Mass: 4066.497 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemically synthesized based on satellite tobacco ringspot virus |
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#2: RNA chain | Mass: 3970.448 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemically synthesized based on satellite tobacco ringspot virus |
#3: RNA chain | Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemically synthesized based on satellite tobacco ringspot virus |
#4: RNA chain | Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemically synthesized based on satellite tobacco ringspot virus |
-Non-polymers , 3 types, 87 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NCO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.8 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 2000 MME, LITHIUM SULFATE, cacodylate, spermidine, cobalt hexaamine, pH 6.0, 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2004 Details: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING |
Radiation | Monochromator: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9764 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30.4 Å / Num. obs: 21699 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 8.2 % / Biso Wilson estimate: 61.8 Å2 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.432 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.093 Å2 / ksol: 0.343432 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→30.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.26 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 4
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Xplor file |
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