+Open data
-Basic information
Entry | Database: PDB / ID: 2lx1 | ||||||||||||||||||
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Title | Major Conformation of the Internal Loop 5'GAGU/3'UGAG | ||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / loop / switch / stacked adenines / inverted sugars | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Authors | Kennedy, S.D. / Turner, D.H. | Citation | Journal: Biochemistry / Year: 2012 | Title: Novel conformation of an RNA structural switch. Authors: Kennedy, S.D. / Kierzek, R. / Turner, D.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lx1.cif.gz | 267.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lx1.ent.gz | 223.7 KB | Display | PDB format |
PDBx/mmJSON format | 2lx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/2lx1 ftp://data.pdbj.org/pub/pdb/validation_reports/lx/2lx1 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 3546.178 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 6.1 / Pressure: ambient / Temperature: 274 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 10 / NA beta-angle constraints total count: 10 / NA chi-angle constraints total count: 22 / NA delta-angle constraints total count: 22 / NA epsilon-angle constraints total count: 12 / NA gamma-angle constraints total count: 20 / NA other-angle constraints total count: 10 / NA sugar pucker constraints total count: 0 / Hydrogen bond constraints total count: 16 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest restraint energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 600 / Conformers submitted total number: 19 / Maximum lower distance constraint violation: 0.03 Å / Maximum upper distance constraint violation: 0.11 Å | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.003 Å |