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- PDB-6ubu: 1.60 A resolution structure of the guanine riboswitch bound to guanine -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ubu | ||||||
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Title | 1.60 A resolution structure of the guanine riboswitch bound to guanine | ||||||
![]() | Guanine riboswitch aptamer domain | ||||||
![]() | RNA / riboswitch aptamer guanine purine nucleobase | ||||||
Function / homology | ACETATE ION / 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 | ![]() | 60.4 KB | Display | ![]() |
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PDB format | ![]() | 37.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 697.4 KB | Display | ![]() |
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Full document | ![]() | 697.8 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uc7C ![]() 6uc8C ![]() 6uc9C ![]() 4fe5S S: Starting model for refinement 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
#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 | #4: Chemical | ChemComp-GUN / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.29 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10 mM potassium HEPES pH 7.5, 20% v/v PEG 3000 MW, 40-50 mM cobalt hexamine, 600-650 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen cryostream / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 25, 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: 1.597→19.66 Å / Num. obs: 37435 / % possible obs: 83.41 % / Redundancy: 4.5 % / Biso Wilson estimate: 20.23 Å2 / Rpim(I) all: 0.061 / Rrim(I) all: 0.131 / Rsym value: 0.131 / Χ2: 2.015 / Net I/σ(I): 13.67 |
Reflection shell | Resolution: 1.597→1.654 Å / Redundancy: 1 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.876 / Num. unique obs: 593 / CC1/2: 0.622 / Χ2: 2.382 / % possible all: 23.15 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FE5 Resolution: 1.6→19.66 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.48 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→19.66 Å
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Refine LS restraints |
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