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- PDB-1jrv: SOLUTION STRUCTURE OF DAATAA DNA BULGE -

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Basic information

Entry
Database: PDB / ID: 1jrv
TitleSOLUTION STRUCTURE OF DAATAA 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*TP*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 (MARDIGRAS); torsion angle dynamics (DYANA); ENERGY MINIMIZATION (AMBER)
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 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 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

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*TP*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)8,8842
Polymers8,8842
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)15 / 400target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 5220.412 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 experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121E-COSY
13331P-1H correlated
NMR detailsText: This structure was determined using standard 2D homonuclear and heteronuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6MM IN DUPLEX; 10MM PHOSPHATE BUFFER; 100MM NACL; 0.05MM EDTA; 100% D2O100% D2O
21.6MM IN DUPLEX; 10MM PHOSPHATE BUFFER; 100MM NACL; 0.05MM EDTA; 90% H2O, 10% D2O90% H2O/10% D2O
31.6MM IN DUPLEX; 100MM NACL; 0.05MM EDTA; 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mm Na+ 7ambient 300 K
2100mm Na+ 7ambient 278 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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002
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
DYANA1.5Gntert, P., Mumenthaler, C., Wthrich, K.structure solution
Amber5Weiner, S.j., Kollman, P.A., Nguyen, D.T., Case, D.A.refinement
Curves4Sklenar, H., Lavery, R.data analysis
Amber5Weiner, S.j., Kollman, P.A., Nguyen, D.T., Case, D.A.data analysis
RefinementMethod: matrix relaxation (MARDIGRAS); torsion angle dynamics (DYANA); ENERGY MINIMIZATION (AMBER)
Software ordinal: 1
Details: the structures are based on a total of 906 restraints, 645 are NOE-derived distance constraints, 235 dihedral angle restraints, 26 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 15

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