[English] 日本語
Yorodumi- PDB-2xsl: The crystal structure of a Thermus thermophilus tRNAGly acceptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xsl | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a Thermus thermophilus tRNAGly acceptor stem microhelix at 1.6 Angstroem resolution | ||||||
Components |
| ||||||
Keywords | RNA / IDENTITY ELEMENTS / GLYCYL-TRNA SYNTHETASE (GLYRS) / RNA HYDRATION | ||||||
Function / homology | : / RNA Function and homology information | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Oberthuer, D. / Eichert, A. / Erdmann, V.A. / Fuerste, J.P. / Betzel, C. / Foerster, C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2011 Title: The Crystal Structure of a Thermus Thermophilus tRNA(Gly) Acceptor Stem Microhelix at 1.6 A Resolution. Authors: Oberthur, D. / Eichert, A. / Erdmann, V.A. / Furste, J.P. / Betzel, C. / Forster, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xsl.cif.gz | 28.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xsl.ent.gz | 18.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/2xsl ftp://data.pdbj.org/pub/pdb/validation_reports/xs/2xsl | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
#1: RNA chain | Mass: 2315.459 Da / Num. of mol.: 2 / Fragment: MICROHELIX, RESIDUES 1-7 / Source method: obtained synthetically / Source: (synth.) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 55979969 #2: RNA chain | Mass: 2132.323 Da / Num. of mol.: 2 / Fragment: MICROHELIX, RESIDUES 66-72 / Source method: obtained synthetically / Source: (synth.) THERMUS THERMOPHILUS (bacteria) / References: GenBank: 55979969 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 62.59 % / Description: NONE |
---|---|
Crystal grow | pH: 7 Details: 0.5 MM RNA IN 40 MM SODIUM CACODYLATE, PH 7.0, 12 MM SPERMINE TETRA-HCL, 80 MM NACL AND 10 % (V/V) MPD, EQUILIBRATED AGAINST 35 % (V/V) MPD, ROOM TEMPERATURE. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→36 Å / Num. obs: 10142 / % possible obs: 94.7 % / Observed criterion σ(I): 1.7 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.7 / % possible all: 72.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ARTIFICIAL RNA Resolution: 1.59→27.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.032 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→27.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|