+Open data
-Basic information
Entry | Database: PDB / ID: 3sux | ||||||
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Title | Crystal structure of THF riboswitch, bound with THF | ||||||
Components | Riboswitch | ||||||
Keywords | RNA / three-way junction / pseudoknot / gene regulator / THF | ||||||
Function / homology | 5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | Eubacterium siraeum V10Sc8a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Huang, L. / Serganov, A. / Patel, D.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch. Authors: Huang, L. / Ishibe-Murakami, S. / Patel, D.J. / Serganov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sux.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sux.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 3sux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/3sux ftp://data.pdbj.org/pub/pdb/validation_reports/su/3sux | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 32837.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA (101-MER) / Source: (synth.) Eubacterium siraeum V10Sc8a (bacteria) |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-THF / |
#4: Water | ChemComp-HOH / |
Sequence details | THE DATABASE REFERENCE CLOSEST TO THE CRYSTALLIZED SEQUENCE IS GB 291556121 (NUCLEOTIDES RANGE: ...THE DATABASE REFERENCE CLOSEST TO THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.66 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Na-HEPES, pH 7.5, 4.2 M Na-formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2011 |
Radiation | Monochromator: SI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 10173 / Num. obs: 10132 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.104 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1008 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 13.212 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.146 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.974 Å / Total num. of bins used: 20
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