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- PDB-1at4: INTRAMOLECULAR DNA TRIPLEX CONTAINING A NON-NUCLEOTIDE LINKER (GA... -

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Basic information

Entry
Database: PDB / ID: 1at4
TitleINTRAMOLECULAR DNA TRIPLEX CONTAINING A NON-NUCLEOTIDE LINKER (GAGAGA-X-TCTCCT-X-CTCTCT), NMR, 7 STRUCTURES
ComponentsDNA (5'-D(*GP*AP*GP*AP*GP*AP*DOP*TP*CP*TP*CP*TP*CP*DOP*CP*TP*CP*TP*CP*T)-3')
KeywordsDNA / INTRAMOLECULAR TRIPLEX / DEOXYRIBONUCLEIC ACID
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsBartley, J.P.
CitationJournal: 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
DepositionAug 18, 1997Processing site: BNL
Revision 1.0Feb 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 23, 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(*GP*AP*GP*AP*GP*AP*DOP*TP*CP*TP*CP*TP*CP*DOP*CP*TP*CP*TP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)5,4431
Polymers5,4431
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)7 / 7LEAST RESTRAINT VIOLATION
Representative

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Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*AP*GP*AP*DOP*TP*CP*TP*CP*TP*CP*DOP*CP*TP*CP*TP*CP*T)-3')


Mass: 5442.527 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DI-(OCTYLPHOSPHATE) LINKER BETWEEN STRANDS 1 AND 2 AND BETWEEN STRANDS 2 AND 3.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY

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Sample preparation

Sample conditionspH: 5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

Software
NameClassification
VNMRmodel building
AMBERrefinement
VNMRphasing
NMR software
NameDeveloperClassification
DiscoverMSIrefinement
VNMRstructure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: RESTRAINED MOLECULAR DYNAMICS USING AMBER FORCEFIELD UNTIL RESIDUAL RESTRAINT ENERGY WAS LESS THAN 1 KCAL MOL-1. THE BEST 12 STRUCTURES HAD PAIRWISE RMSD OF 0.51 A. INSIGHT ALSO WAS USED.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 7 / Conformers submitted total number: 7

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