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Open data
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Basic information
Entry | Database: PDB / ID: 2eeu | ||||||
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Title | Guanine riboswitch U22A, A52U mutant bound to hypoxanthine | ||||||
![]() | Guanine riboswitch | ||||||
![]() | RNA / mRNA / riboswitch / guanine / hypoxanthine / RNA-ligand complex / three-way junction / double helix | ||||||
Function / homology | ACETATE ION / HYPOXANTHINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gilbert, S.D. / Love, C.E. / Batey, R.T. | ||||||
![]() | ![]() Title: Mutational analysis of the purine riboswitch aptamer domain Authors: Gilbert, S.D. / Love, C.E. / Edwards, A.L. / Batey, R.T. | ||||||
History |
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Remark 999 | SEQUENCE Residues A22 and U52 were engineered from U and A, respectively, based on the guanine ...SEQUENCE Residues A22 and U52 were engineered from U and A, respectively, based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56 KB | Display | ![]() |
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PDB format | ![]() | 39.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
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Full document | ![]() | 443.4 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2eesC ![]() 2eetC ![]() 2eevC ![]() 2eewC ![]() 1u8d C: citing same article ( S: Starting model for refinement |
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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
#1: RNA chain | Mass: 21506.783 Da / Num. of mol.: 1 / Mutation: U22A, A52U / Source method: obtained synthetically Details: This sequence was engineered based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis. References: ![]() | ||||
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#2: Chemical | ChemComp-ACT / | ||||
#3: Chemical | ChemComp-NCO / #4: Chemical | ChemComp-HPA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.41 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% Polyethylene glycol 3000, 480mM ammonium acetate, 10mM cobalt hexammine chloride, 10mM K(+)-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2006 |
Radiation | Monochromator: Nickel Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 14514 / Num. obs: 13890 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.11 % / Biso Wilson estimate: 23.7 Å2 / Rsym value: 0.067 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 6.21 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 1180 / Rsym value: 0.262 / % possible all: 82 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1U8D ![]() 1u8d Resolution: 1.95→18.91 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 450169.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→18.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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