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- PDB-1rvi: SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG -

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Basic information

Entry
Database: PDB / ID: 1rvi
TitleSOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG
Components5'-D(*CP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*G)-3'
KeywordsDNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, for details see (Padrta et al. (2002) J. Biomol. NMR 24, 1-24)
AuthorsStefl, R. / Wu, H. / Ravindranathan, S. / Sklenar, V. / Feigon, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum.
Authors: Stefl, R. / Wu, H. / Ravindranathan, S. / Sklenar, V. / Feigon, J.
History
DepositionDec 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,3232
Polymers7,3232
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 30structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*CP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*G)-3'


Mass: 3661.416 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2223D 13C-separated NOESY
131DQF-COSY
14231P spin-echo diff CT-HSQC
152spin-echo diff CH-(H)CCH
161HSQC (with and without Pf1 phage)
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING RESIDUAL DIPOLAR COUPLINGS

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM (in duplex) CGTTTTAAAACG, 25mM NH4Cl, 100% D2O or 90% H2O/10% D2Oeither 100% D2O or 90% H2O/10% D2O
22mM (in duplex) CGTTTTAAAACG, U-13C,15N, 25mM NH4Cl, 100% D2O100% D2O
Sample conditionsIonic strength: 25 mM NH4Cl / pH: 6.0 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR softwareName: Amber / Version: 7 / Developer: CASE, D.A., et al. / Classification: refinement
RefinementMethod: simulated annealing, for details see (Padrta et al. (2002) J. Biomol. NMR 24, 1-24)
Software ordinal: 1
Details: the structures are based on a total of 833 restraints, 549 are NOE-derived distance restraints, 160 torsion angle restraints, 24 pseudorotation phase angle restraints, 24 distance restraints ...Details: the structures are based on a total of 833 restraints, 549 are NOE-derived distance restraints, 160 torsion angle restraints, 24 pseudorotation phase angle restraints, 24 distance restraints from W-C hydrogen bonds, and 72 residual dipolar couplings.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 9

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