+Open data
-Basic information
Entry | Database: PDB / ID: 2b57 | ||||||
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Title | Guanine Riboswitch C74U mutant bound to 2,6-diaminopurine | ||||||
Components | 65-MER | ||||||
Keywords | RNA / RNA-ligand complex / Double helix / base triples / base quadruples / mRNA / purine | ||||||
Function / homology | 9H-PURINE-2,6-DIAMINE / ACETATE ION / COBALT HEXAMMINE(III) / : / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Gilbert, S.D. / Stoddard, C.D. / Wise, S.J. / Batey, R.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. Authors: Gilbert, S.D. / Stoddard, C.D. / Wise, S.J. / 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 | 2b57.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b57.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 2b57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b57_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 2b57_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 2b57_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 2b57_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/2b57 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/2b57 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 20857.381 Da / Num. of mol.: 1 / Fragment: G-box RNA / Mutation: C74U / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription. The sequence of this RNA can be found naturally in Bacillus Subtilis References: GenBank: 1256615 | ||||
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#2: Chemical | ChemComp-ACT / | ||||
#3: Chemical | ChemComp-NCO / #4: Chemical | ChemComp-6AP / | #5: 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: 2.29 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 2K, 480 mM Ammonium Acetate, 12 mM Cobalt Hexammine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 18, 2005 |
Radiation | Monochromator: NI Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. all: 10478 / Num. obs: 10387 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 17.7 Å2 |
Reflection shell | Resolution: 2.15→2.23 Å / % possible all: 90.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→19.86 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 423665.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.7638 Å2 / ksol: 0.352404 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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