[English] 日本語
Yorodumi- PDB-3gx5: Crystal structure of T. tencongensis SAM-I riboswitch variant A94... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gx5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T. tencongensis SAM-I riboswitch variant A94G/U34 bound with SAM | ||||||
Components | RNA (94-MER) | ||||||
Keywords | RNA / kink-turn / pseudoknot / four-way junction / riboswitch | ||||||
Function / homology | : / S-ADENOSYLMETHIONINE / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gx5.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gx5.ent.gz | 96.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gx5 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gx5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3gx2C 3gx3C 3gx6C 3gx7C 2gisS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 occuring sequence found in T. tengcongensis | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SAM / | ||||
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 mM magnesium chloride, 80 mM potassium chloride, 16 mM spermine-HCl, 8% MPD, 40 mM cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 12862 / Num. obs: 12862 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 16.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.4 / % possible all: 87.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2GIS Resolution: 2.402→19.835 Å / SU ML: 0.36 / σ(F): 0.09 / Phase error: 28.88 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.682 Å2 / ksol: 0.284 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.402→19.835 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 10.5538 Å / Origin y: -9.7835 Å / Origin z: 16.2974 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |