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Yorodumi- PDB-3fo4: Crystal structure of guanine riboswitch C74U mutant bound to 6-ch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fo4 | ||||||
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Title | Crystal structure of guanine riboswitch C74U mutant bound to 6-chloroguanine | ||||||
Components | Guanine riboswitch C74U mutant | ||||||
Keywords | RNA / mRNA / riboswitch / 6-chloroguanine / adenine / RNA-ligand complex / double helix / three-way junction | ||||||
Function / homology | 6-chloroguanine / ACETATE ION / COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gilbert, S.D. / Batey, R.T. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Adaptive ligand binding by the purine riboswitch in the recognition of Guanine and adenine analogs. Authors: Gilbert, S.D. / Reyes, F.E. / Edwards, A.L. / 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 | 3fo4.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fo4.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/3fo4 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/3fo4 | HTTPS FTP |
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-Related structure data
Related structure data | 3fo6C 3g4mC 3gaoC 3gerC 3gesC 3gogC 3gotC 1u8d 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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Details | The asymmetric unit contains one biological unit |
-Components
#1: RNA chain | Mass: 21836.975 Da / Num. of mol.: 1 / Mutation: C74U / Source method: obtained synthetically Details: This sequence was engineered based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis | ||
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#2: Chemical | ChemComp-6GU / | ||
#3: Chemical | ChemComp-ACT / | ||
#4: Chemical | ChemComp-NCO / #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: 2.23 Å3/Da / Density % sol: 44.87 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 2000, 480 mM Ammonium acetate, 12 mM Cobalt hexammine, 10 mM K+HEPES, 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: May 13, 2005 |
Radiation | Monochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 16673 / Num. obs: 15304 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.56 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.31 % / Rsym value: 0.201 / % possible all: 69.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1U8D 1u8d Resolution: 1.9→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1233811.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.9172 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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