+Open data
-Basic information
Entry | Database: PDB / ID: 3fu2 | ||||||
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Title | Cocrystal structure of a class-I preQ1 riboswitch | ||||||
Components | PreQ1 riboswitch | ||||||
Keywords | RNA / aptamer / riboswitch / queuosine / PreQ1 | ||||||
Function / homology | 7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Klein, D.J. / Edwards, T.E. / Ferre-D'Amare, A.R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase Authors: Klein, D.J. / Edwards, T.E. / Ferre-D'Amare, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fu2.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fu2.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/3fu2 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/3fu2 | 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 10835.524 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: Chemically synthesized RNA corresponding to the natural sequence from Bacillus subtilis #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.86 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% PEG 550 MME, 50 mM CaCl2, 100 mM Hepes-KOH pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→30 Å / Num. all: 7147 / Num. obs: 7147 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.126 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 68.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→30 Å
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Refine LS restraints |
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