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- PDB-1qsk: NMR-DERIVED SOLUTION STRUCTURE OF A FIVE-ADENINE BULGE LOOP WITHI... -

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Basic information

Entry
Database: PDB / ID: 1qsk
TitleNMR-DERIVED SOLUTION STRUCTURE OF A FIVE-ADENINE BULGE LOOP WITHIN A DNA DUPLEX
Components
  • 5'-D(CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*CP)-3'
  • 5'-D(GP*CP*AP*TP*CP*GP*AP*AP*AP*AP*AP*GP*CP*TP*AP*CP*GP)-3'
KeywordsDNA / DNA BULGE / FIVE-ADENINE BULGE LOOP
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION
AuthorsDornberger, U. / Hillisch, A. / Gollmick, F. / Fritzsche, H. / Diekmann, S.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structure of a five-adenine bulge loop within a DNA duplex.
Authors: Dornberger, U. / Hillisch, A. / Gollmick, F.A. / Fritzsche, H. / Diekmann, S.
History
DepositionJun 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,8932
Polymers8,8932
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)15 / 600target function
RepresentativeModel #6fewest violations

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Components

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


Mass: 5229.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ARTIFICIAL SEQUENCE
#2: DNA chain 5'-D(CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*CP)-3'


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131E-COSY
141P-COSY
2522D NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

Details
Solution-IDContents
12.8MM IN DUPLEX; 10MM PHOSPHATE BUFFER, 100MM NACL, 0.05MM EDTA, 100% D2O
22.8MM IN DUPLEX; 10MM PHOSPHATE BUFFER, 100MM NACL, 0.05MM EDTA, 90% H2O,10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NACL 7.0 AMBIENT 300 K
2100mM NACL 7.0 AMBIENT 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian UNITYVarianUNITY5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4.3VARIANcollection
NMRPipe1.7DELAGLIOprocessing
MARDIGRAS3.2BORGIAS & JAMESiterative matrix relaxation
DYANA1.5GUNTERTstructure solution
Amber5pearlmanstructure solution
Amber5pearlmanrefinement
RefinementMethod: TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 15

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