+Open data
-Basic information
Entry | Database: PDB / ID: 6uc8 | ||||||
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Title | Guanine riboswitch bound to 8-aminoguanine | ||||||
Components | Guanine riboswitch | ||||||
Keywords | RNA / riboswitch aptamer guanine purine nucleobase / 8-aminoguanine | ||||||
Function / homology | ACETATE ION / 8-AMINOGUANINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.898 Å | ||||||
Authors | Matyjasik, M.M. / Hall, S.D. / Batey, R.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Molecules / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uc8.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uc8.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 6uc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uc8_validation.pdf.gz | 335.9 KB | Display | wwPDB validaton report |
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Full document | 6uc8_full_validation.pdf.gz | 336.7 KB | Display | |
Data in XML | 6uc8_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6uc8_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/6uc8 ftp://data.pdbj.org/pub/pdb/validation_reports/uc/6uc8 | HTTPS FTP |
-Related structure data
Related structure data | 6ubuC 6uc7C 6uc9C 4fe5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Bacillus subtilis (bacteria) | ||||||
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#2: Chemical | ChemComp-ANG / | ||||||
#3: Chemical | ChemComp-NCO / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
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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, 35-47 mM cobalt hexamine, and 600 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.898→19.96 Å / Num. obs: 13646 / % possible obs: 87.57 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.49 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.04 / Rrim(I) all: 0.083 / Rsym value: 0.073 / Χ2: 1.84 / Net I/σ(I): 16.75 |
Reflection shell | Resolution: 1.898→1.966 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 1.506 / Num. unique obs: 572 / CC1/2: 0.9 / Rpim(I) all: 0.193 / Rrim(I) all: 0.3 / Rsym value: 0.228 / Χ2: 1.84 / % possible all: 36.89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FE5 Resolution: 1.898→19.956 Å / Cross valid method: FREE R-VALUE / Phase error: 26.62
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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: 1.898→19.956 Å
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LS refinement shell | Resolution: 1.898→1.9367 Å /
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