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- PDB-1d3x: INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1d3x
TitleINTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES
Components
  • DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*A)-3')
  • DNA (5'-D(*TP*CP*TP*CP*TP*CP*TP*T)-3')
  • DNA (5'-D(*TP*TP*CP*TP*CP*TP*CP*T)-3')
KeywordsDNA / OLIGONUCLEOTIDE / TRIPLEX / RNA THIRD STRAND
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsTarkoy, M. / Phipps, A.K. / Schultze, P. / Feigon, J.
CitationJournal: Biochemistry / Year: 1998
Title: Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT).
Authors: Tarkoy, M. / Phipps, A.K. / Schultze, P. / Feigon, J.
History
DepositionFeb 5, 1998Processing site: BNL
Revision 1.0May 6, 1998Provider: 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: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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(*AP*GP*AP*GP*AP*GP*AP*A)-3')
B: DNA (5'-D(*TP*TP*CP*TP*CP*TP*CP*T)-3')
C: DNA (5'-D(*TP*CP*TP*CP*TP*CP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,1963
Polymers7,1963
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 / 20LOWEST OVERALL ENERGY
Representative

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Components

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


Mass: 2508.694 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 AND BETWEEN T 16 AND T 17, C 18, C 20, AND C 22 ARE PROTONATED AT N3
#2: DNA chain DNA (5'-D(*TP*TP*CP*TP*CP*TP*CP*T)-3')


Mass: 2343.552 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 AND BETWEEN T 16 AND T 17, C 18, C 20, AND C 22 ARE PROTONATED AT N3
#3: DNA chain DNA (5'-D(*TP*CP*TP*CP*TP*CP*TP*T)-3')


Mass: 2343.552 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 AND BETWEEN T 16 AND T 17, C 18, C 20, AND C 22 ARE PROTONATED AT N3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131TOCSY-NOESY
141HSQC
151DQF-COSY

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Sample preparation

Sample conditionspH: 5.7 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE GN500GEGN5005001
Bruker AMX500BrukerAMX5005002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: LAST REFINEMENT STEP USED RELAXATION MATRIX REFINEMENT.
NMR ensembleConformer selection criteria: LOWEST OVERALL ENERGY / Conformers calculated total number: 20 / Conformers submitted total number: 10

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