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- PDB-1nev: A-tract decamer -

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Basic information

Entry
Database: PDB / ID: 1nev
TitleA-tract decamer
Components
  • 5'-D(*CP*CP*GP*TP*TP*TP*TP*GP*CP*C)-3'
  • 5'-D(*GP*GP*CP*AP*AP*AP*AP*CP*GP*G)-3'
KeywordsDNA / A-tract / DNA bending / DNA decamer
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / Torsion angle + Cartesian simulated annealing. Then cartesian refinement with dipolar couplings.
AuthorsBarbic, A. / Zimmer, D.P. / Crothers, D.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structural origins of adenine-tract bending
Authors: Barbic, A. / Zimmer, D.P. / Crothers, D.M.
History
DepositionDec 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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: 5'-D(*GP*GP*CP*AP*AP*AP*AP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*TP*TP*TP*TP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
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)10 / 30structures with the lowest energy
Representative

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Components

#1: DNA chain 5'-D(*GP*GP*CP*AP*AP*AP*AP*CP*GP*G)-3' / A4


Mass: 3103.057 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Phosphoramidite synthesis, and Zimmer and Crothers PNAS 92, 3091-5 (1995)
#2: DNA chain 5'-D(*CP*CP*GP*TP*TP*TP*TP*GP*CP*C)-3'


Mass: 2986.953 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Phosphoramidite synthesis, and Zimmer and Crothers PNAS 92, 3091-5 (1995)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131(H)CCH-E.COSY
141(H)CCH-COSY
151HSQC
161(H)CCH-TOCSY
NMR detailsText: Dipolar couplings measured in 22 mg/ml bacteriophage Pf1. Structures superimposed over inner 8 bp.

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Sample preparation

DetailsContents: 200 mM NaCl, 20 mM sodium phosphate (pH=7.0), 0.5 mM EDTA
Solvent system: water
Sample conditionsIonic strength: 200 mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 298 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
Varian INOVAVarianINOVA8001
Varian UNITYPLUSVarianUNITYPLUS6002
Varian UNITYVarianUNITY5003
GE OMEGAGEOMEGA5004
Varian INOVAVarianINOVA5005

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Processing

NMR software
NameVersionDeveloperClassification
Felix95Molec. Symulationsdata analysis
CNS1Brunger et al.structure solution
CNS1Brunger et al.refinement
YARMLapham, J.iterative matrix relaxation
RefinementMethod: Torsion angle + Cartesian simulated annealing. Then cartesian refinement with dipolar couplings.
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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