+Open data
-Basic information
Entry | Database: PDB / ID: 4lvx | ||||||
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Title | Structure of the THF riboswitch bound to tetrahydrobiopterin | ||||||
Components | THF riboswitch | ||||||
Keywords | RNA / Aptamers / Nucleotide / Bacillus subtilis / Bacterial Proteins / Base Sequence / Binding Sites / Calorimetry / Folic Acid / Gene Expression Regulation / Bacterial / Guanine / Leucovorin / Ligands / Magnesium / Molecular Sequence Data / Nucleic Acid Conformation / Point Mutation / Protein Binding / Protein Structure / Secondary / Riboswitch / S-Adenosylmethionine / Streptococcus mutans / Terminator Regions / Genetic / Tetrahydrofolates / Thermodynamics / Transcription / three-way junction / pseudoknot / regulation / ncRNA / tetrahydrobiopterin binding / mRNA | ||||||
Function / homology | 5,6,7,8-TETRAHYDROBIOPTERIN / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Trausch, J.J. / Batey, R.T. | ||||||
Citation | Journal: Chem.Biol. / Year: 2014 Title: A Disconnect between High-Affinity Binding and Efficient Regulation by Antifolates and Purines in the Tetrahydrofolate Riboswitch. Authors: Trausch, J.J. / Batey, R.T. #1: Journal: Structure / Year: 2011 Title: The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Authors: Trausch, J.J. / Ceres, P. / Reyes, F.E. / 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 | 4lvx.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lvx.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 4lvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lvx_validation.pdf.gz | 404.4 KB | Display | wwPDB validaton report |
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Full document | 4lvx_full_validation.pdf.gz | 406.5 KB | Display | |
Data in XML | 4lvx_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 4lvx_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/4lvx ftp://data.pdbj.org/pub/pdb/validation_reports/lv/4lvx | HTTPS FTP |
-Related 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: 28849.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 in vitro transcribed | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2,4-methyl-pentanediol, spermine, sodium cacodylate, sodium chloride, dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1051 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1051 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→52.69 Å / Num. all: 24030 / % possible obs: 99.4 % / Observed criterion σ(F): 5.5 / Observed criterion σ(I): 5.5 / Redundancy: 5.7 % |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.109 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.751 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 30.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.751 Å
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Refine LS restraints |
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LS refinement shell |
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