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- PDB-1t4x: The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 ... -

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Basic information

Entry
Database: PDB / ID: 1t4x
TitleThe first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt
ComponentsRNA (5'-R(*CP*GP*CP*GP*CP*G)-3')
KeywordsRNA / LEFT-HANDED RNA DUPLEX / Z-RNA
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics with NMR restraints
AuthorsPopenda, M. / Milecki, J. / Adamiak, R.W.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: High salt solution structure of a left-handed RNA double helix.
Authors: Popenda, M. / Milecki, J. / Adamiak, R.W.
History
DepositionApr 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*GP*CP*G)-3')
B: RNA (5'-R(*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,8122
Polymers3,8122
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*CP*GP*CP*GP*CP*G)-3')


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
13131P-1H HETCOR

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Sample preparation

DetailsContents: 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%)
Sample conditionsIonic strength: 6M NaClO4 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
Felix2000Accelrysdata analysis
CYANA1Guentertstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 12

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