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- PDB-1bce: INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1bce
TitleINTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES
Components
  • DNA (5'-D(*AP*AP*GP*GP*AP*A)-3')
  • DNA (5'-D(*TP*TP*CP*CP*TP*T)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DNA TRIPLEX
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsAsensio, J.L. / Brown, T. / Lane, A.N.
Citation
Journal: Nucleic Acids Res. / Year: 1998
Title: Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets.
Authors: Asensio, J.L. / Brown, T. / Lane, A.N.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: The Contribution of Cytosine Protonation to the Stability of Parallel DNA Triple Helices
Authors: Asensio, J.L. / Lane, A.N. / Dhesi, J. / Bergqvist, S. / Brown, T.
History
DepositionApr 29, 1998Processing site: BNL
Revision 1.0Aug 12, 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: 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

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Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*GP*GP*AP*A)-3')
B: DNA (5'-D(*TP*TP*CP*CP*TP*T)-3')
C: DNA (5'-D(*TP*TP*CP*CP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)5,3673
Polymers5,3673
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 / 50ENERGY, NMR R FACTORS
Representative

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Components

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


Mass: 1866.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICAL SYNTHESIS
#2: DNA chain DNA (5'-D(*TP*TP*CP*CP*TP*T)-3')


Mass: 1750.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICAL SYNTHESIS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
NMR detailsText: THE STRUCTURES WERE BASED ON ANALYSIS OF SCALAR COUPLING CONSTANTS AND DISTANCES DERIVED FROM TIME-DEPENDENT NOES USING RESTRAINED MOLECULAR DYNAMICS.

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Sample preparation

DetailsContents: H2O
Sample conditionsIonic strength: 0.1M / pH: 5 / Pressure: 1 ATMOSPHERE / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameDeveloperClassification
DiscoverMSIrefinement
Discoverstructure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 / Details: RESTRAINED MD/SIMULATED ANNEALING PROTOCOL
NMR ensembleConformer selection criteria: ENERGY, NMR R FACTORS / Conformers calculated total number: 50 / Conformers submitted total number: 10

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