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Yorodumi- PDB-3gx3: Crystal structure of the T. tengcongensis SAM-I riboswitch varian... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gx3 | ||||||
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Title | Crystal structure of the T. tengcongensis SAM-I riboswitch variant U34C/A94G bound with SAH | ||||||
Components | RNA (94-MER) | ||||||
Keywords | RNA / kink-turn / four-way junction / pseudoknot / riboswitch | ||||||
Function / homology | : / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Montange, R.K. / Batey, R.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch. Authors: Montange, R.K. / Mondragon, E. / van Tyne, D. / Garst, A.D. / Ceres, P. / 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 | 3gx3.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gx3.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gx3 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gx3 | HTTPS FTP |
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-Related structure data
Related structure data | 3gx2C 3gx5C 3gx6C 3gx7C 2gisS 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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-Components
#1: RNA chain | Mass: 30568.338 Da / Num. of mol.: 1 / Mutation: U34C, A94G / Source method: obtained synthetically Details: the sequence is based on a naturally occurring sequence found in T. tengcongensis | ||||
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#2: Chemical | ChemComp-SAH / | ||||
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-K / | #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: 2.52 Å3/Da / Density % sol: 51.22 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: 20 mM magnesium chloride, 80 mM potassium chloride, 12 mM spermine, 10% MPD, 40 mM cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||
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 RUH2R / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 19, 2009 / Details: osmic mirror |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 8993 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 6.74 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.06 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 4.6 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2GIS Resolution: 2.7→19.741 Å / SU ML: 0.54 / σ(F): 2.2 / Phase error: 33.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.38 Å2 / ksol: 0.245 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.741 Å
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Refine LS restraints |
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LS refinement shell |
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