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Open data
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Basic information
Entry | Database: PDB / ID: 6uc9 | ||||||
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Title | Guanine riboswitch bound to O6-cyclohexylmethyl guanine | ||||||
![]() | Guanine riboswitch | ||||||
![]() | RNA / riboswitch aptamer guanine purine nucleobase / O6-methylcyclohexyl guanine | ||||||
Function / homology | ACETATE ION / 6-O-CYCLOHEXYLMETHYL GUANINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Matyjasik, M.M. / Batey, R.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High Affinity Binding of N2-Modified Guanine Derivatives Significantly Disrupts the Ligand Binding Pocket of the Guanine Riboswitch. Authors: Matyjasik, M.M. / Hall, S.D. / 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 | ![]() | 55.9 KB | Display | ![]() |
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PDB format | ![]() | 37.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 768.4 KB | Display | ![]() |
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Full document | ![]() | 771 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ubuC ![]() 6uc7C ![]() 6uc8C ![]() 4fe5S 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 / Source: (synth.) ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-NCO / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-CMG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 10 mM potassium HEPES pH 7.5, 22.6% v/v PEG 3000 MW, 35-45 mM cobalt hexamine, and 600-650 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 20, 2019 |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.941→19.86 Å / Num. obs: 14355 / % possible obs: 97.91 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.064 / Rrim(I) all: 0.171 / Rsym value: 0.158 / Χ2: 1.041 / Net I/σ(I): 11.96 |
Reflection shell | Resolution: 1.941→2.011 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.085 / Num. unique obs: 1226 / CC1/2: 0.588 / Rpim(I) all: 0.248 / Rrim(I) all: 0.513 / Rsym value: 0.445 / Χ2: 0.536 / % possible all: 85.26 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FE5 Resolution: 1.941→19.86 Å / Cross valid method: FREE R-VALUE / Phase error: 22.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.24 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.941→19.86 Å
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LS refinement shell | Resolution: 1.941→1.976 Å /
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