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Open data
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Basic information
Entry | Database: PDB / ID: 2eet | ||||||
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Title | Guanine Riboswitch A21G, U75C mutant bound to hypoxanthine | ||||||
![]() | Guanine Riboswitch | ||||||
![]() | RNA / mRNA / riboswitch / hypoxanthine / guanine / RNA-ligand complex / double helix / three-way junction / base triple | ||||||
Function / homology | ACETATE ION / HYPOXANTHINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gilbert, S.D. / Edwards, A.L. / 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 G21 and C75 were engineered from A and U, respectively, based on the guanine ...SEQUENCE Residues G21 and C75 were engineered from A and U, 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 | ![]() | 57.1 KB | Display | ![]() |
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PDB format | ![]() | 40 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.1 KB | Display | ![]() |
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Full document | ![]() | 444.2 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2eesC ![]() 2eeuC ![]() 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: 21521.801 Da / Num. of mol.: 1 / Mutation: A21G, U75C / Source method: obtained synthetically Details: This sequence was engineered based on the guanine riboswitch 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: 2.28 Å3/Da / Density % sol: 46.15 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% Polyethylene glycol 3000, 400mM ammonium acetate, 12mM cobalt hexammine chloride, 10 mM 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 / Detector: IMAGE PLATE / Date: Jun 27, 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→19.95 Å / Num. all: 13552 / Num. obs: 13407 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.26 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.13 % / Mean I/σ(I) obs: 6 / Num. unique all: 1018 / Rsym value: 0.15 / % possible all: 71.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1U8D ![]() 1u8d Resolution: 1.95→19.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1332366.22 / 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: 26.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→19.95 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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