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- PDB-1js5: Solution Structure of dAAUAA DNA Bulge -

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Basic information

Entry
Database: PDB / ID: 1js5
TitleSolution Structure of dAAUAA DNA Bulge
Components
  • 5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*UP*AP*AP*GP*CP*TP*AP*CP*G)-3'
KeywordsDNA / DNA bulge / five-nucleotide bulge loop / deoxyribonucleic acid
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / matrix relaxation, torsion angle dynamics, energy minimization
Model type detailsminimized average
AuthorsGollmick, F.A. / Lorenz, M. / Dornberger, U. / von Langen, J. / Diekmann, S. / Fritzsche, H.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: Solution structure of dAATAA and dAAUAA DNA bulges.
Authors: Gollmick, F.A. / Lorenz, M. / Dornberger, U. / von Langen, J. / Diekmann, S. / Fritzsche, H.
History
DepositionAug 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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*CP*AP*TP*CP*GP*AP*AP*UP*AP*AP*GP*CP*TP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)8,8702
Polymers8,8702
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)1 / -
Representativeminimized average structure

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Components

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


Mass: 5206.386 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3'


Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. This structure was determined using standard 2D ...Text: THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. This structure was determined using standard 2D homonuclear and heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
13.8mm in duplex; 10mm phosphate buffer; 100 mm NaCl; 0.05mm EDTA, 100% D2O100% D2O
23.8mm in duplex; 100 mm NaCl; 0.05mm EDTA, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mm Na+ 7ambient 300 K
2100mm Na+ 7ambient 300 K

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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 INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Delaglio, F., et al.processing
MARDIGRAS3.2Borgias, B.A:, James, T.L.iterative matrix relaxation
DYANA1.5Guentert, P., Mumenthaler, C., Wuetrich, K.structure solution
Amber5Weiner, S.j., Kollman, P.A., Nguyen, D.T., Case, D.A.refinement
Amber5Weiner, S.j., Kollman, P.A., Nguyen, D.T., Case, D.A.data analysis
RefinementMethod: matrix relaxation, torsion angle dynamics, energy minimization
Software ordinal: 1
Details: the structures are based on a total of 932 restraints, 671 are NOE-derived distance constraints, 235 dihedral angle restraints,26 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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