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Yorodumi- PDB-4fen: Crystal structure of the A24U/U25A/A46G mutant xpt-pbuX guanine r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fen | ||||||
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Title | Crystal structure of the A24U/U25A/A46G mutant xpt-pbuX guanine riboswitch aptamer domain in complex with hypoxanthine | ||||||
Components | A24U/U25A/A46G mutant of the B. subtilis xpt-pbuX guanine riboswitch aptamer domain | ||||||
Keywords | RNA / three-way junction with distal tertiary interaction / genetic regulatory element | ||||||
Function / homology | ACETATE ION / HYPOXANTHINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Stoddard, C.D. / Trausch, J.J. / Widmann, J. / Marcano, J. / Knight, R. / Batey, R.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch. Authors: Stoddard, C.D. / Widmann, J. / Trausch, J.J. / Marcano-Velazquez, J.G. / Knight, R. / 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 | 4fen.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fen.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 4fen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/4fen ftp://data.pdbj.org/pub/pdb/validation_reports/fe/4fen | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 21522.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 RNAP transcript | ||
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#2: Chemical | ChemComp-HPA / | ||
#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: 2.27 Å3/Da / Density % sol: 45.84 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 3K, 200 mM ammonium acetate, 10 mM cobalt hexammine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40 Å / Num. all: 42755 / Num. obs: 40660 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.35→1.37 Å / % possible all: 66.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.13 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.1 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→40 Å
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Refine LS restraints |
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