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- PDB-1t4x: The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1t4x | ||||||||||||||||||
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Title | The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt | ||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / LEFT-HANDED RNA DUPLEX / Z-RNA | Function / homology | RNA | ![]() Method | SOLUTION NMR / molecular dynamics with NMR restraints | ![]() Popenda, M. / Milecki, J. / Adamiak, R.W. | ![]() ![]() Title: High salt solution structure of a left-handed RNA double helix. Authors: Popenda, M. / Milecki, J. / Adamiak, R.W. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.2 KB | Display | ![]() |
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PDB format | ![]() | 55.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 316.2 KB | Display | ![]() |
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Full document | ![]() | 392 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: RNA chain | Mass: 1906.205 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: automated solid-phase synthesis using 2'-O-tBDMSi-protected ribonucleoside phoshoramidites. |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: RNA (2-3 mM) in buffer containing 150 mM NaCl, 10 mM sodium phosphate pH 6.5, 0.1 mM EDTA and 6M NaClO4 Solvent system: D2O (99.98%) |
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Sample conditions | Ionic strength: 6M NaClO4 / pH: 6.5 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: molecular dynamics with NMR restraints / Software ordinal: 1 Details: NMR refinement using X-PLOR, NOE intra-residue distances 120, NOE inter-residue distances 112, Dihedral angle restraints 100, Watson-Crick pair distances 18, Planarity of base pairs - 6. ...Details: NMR refinement using X-PLOR, NOE intra-residue distances 120, NOE inter-residue distances 112, Dihedral angle restraints 100, Watson-Crick pair distances 18, Planarity of base pairs - 6. Total restraints/residue: 30 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 12 |