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Open data
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Basic information
Entry | Database: PDB / ID: 3g4m | ||||||
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Title | Crystal structure of guanine riboswitch bound to 2-aminopurine | ||||||
![]() | Guanine riboswitch | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | 9H-purin-2-amine / ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gilbert, S.D. / Batey, R.T. | ||||||
![]() | ![]() Title: Adaptive ligand binding by the purine riboswitch in the recognition of Guanine and adenine analogs. Authors: Gilbert, S.D. / Reyes, F.E. / Edwards, A.L. / Batey, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.1 KB | Display | ![]() |
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PDB format | ![]() | 35.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fo4C ![]() 3fo6C ![]() 3gaoC ![]() 3gerC ![]() 3gesC ![]() 3gogC ![]() 3gotC ![]() 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 / 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. | ||
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#2: Chemical | ChemComp-2BP / ![]() | ||
#3: Chemical | ChemComp-ACT / ![]() | ||
#4: Chemical | ChemComp-NCO / #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3K, 12.5 mM cobalt hexammine, 600mM ammonium acetate, 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 IV / Detector: IMAGE PLATE / Date: Nov 17, 2008 |
Radiation | Monochromator: Nickel Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→19.92 Å / Num. obs: 13481 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 1.83 % / Rsym value: 0.08 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 1.64 % / Mean I/σ(I) obs: 3 / Rsym value: 0.284 / % possible all: 86 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1U8D ![]() 1u8d Resolution: 2.4→19.92 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 320880.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.0612 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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