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- PDB-1bwg: DNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1bwg
TitleDNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURES
Components
  • DNA (5'-D(*CP*TP*CP*TP*CP*T)-3')
  • DNA (5'-D(*GP*AP*CP*TP*GP*AP*GP*AP*GP*AP*CP*GP*TP*A)-3')
  • DNA (5'-D(*TP*AP*CP*GP*TP*CP*TP*CP*TP*CP*AP*GP*TP*C)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DNA TRIPLEX / TRIPLEX-DUPLEX JUNCTIONS
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsAsensio, J.L. / Brown, T. / Lane, A.N.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Solution conformation of a parallel DNA triple helix with 5' and 3' triplex-duplex junctions.
Authors: Asensio, J.L. / Brown, T. / Lane, A.N.
#1: Journal: Biochemistry / Year: 1997
Title: Solution Conformation of an Intramolecular DNA Triplex Containing a Nonnucleotide Linker: Comparison with the DNA Duplex
Authors: Bartley, J.P. / Brown, T. / Lane, A.N.
History
DepositionSep 22, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: DNA (5'-D(*GP*AP*CP*TP*GP*AP*GP*AP*GP*AP*CP*GP*TP*A)-3')
B: DNA (5'-D(*TP*AP*CP*GP*TP*CP*TP*CP*TP*CP*AP*GP*TP*C)-3')
C: DNA (5'-D(*CP*TP*CP*TP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)10,2963
Polymers10,2963
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 / 30LEAST RESTRAINT VIOLATIONS
Representative

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Components

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


Mass: 4353.854 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*CP*GP*TP*CP*TP*CP*TP*CP*AP*GP*TP*C)-3')


Mass: 4206.740 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*TP*CP*TP*CP*T)-3')


Mass: 1735.166 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
111NOESY DQF-COSY
121ROESY
13113C-HSQC
NMR detailsText: THE STRUCTURES WERE DETERMINED FROM NOE AND J-COUPLING DATA ON TWO INTRAMOLECULAR DNA TRIPLE HELICES CONTAINING IDENTICAL CORE SEGMENTS. THE RESTRAINTS WERE GENERATED FOR THE SUPERMOLECULE ...Text: THE STRUCTURES WERE DETERMINED FROM NOE AND J-COUPLING DATA ON TWO INTRAMOLECULAR DNA TRIPLE HELICES CONTAINING IDENTICAL CORE SEGMENTS. THE RESTRAINTS WERE GENERATED FOR THE SUPERMOLECULE CONTAINING THE CORE TRIPLEX REGION AND THE 5' AND 3' DUPLEX EXTEN SIONS.

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Sample preparation

Sample conditionsIonic strength: 0.1 / pH: 5 / Pressure: 1 atm / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameDeveloperClassification
DiscoverBIOSYMrefinement
Discoverstructure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 / Details: RESTRAINED MD
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers calculated total number: 30 / Conformers submitted total number: 10

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