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- PDB-1aul: SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A ... -

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Basic information

Entry
Database: PDB / ID: 1aul
TitleSOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE
Components
  • DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*THXP*GP*AP*TP*TP*AP*TP*CP*TP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / CDPI3
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, RELAXATION MATRIX REFINEMENT
AuthorsKumar, S. / Reed, M.W. / Gamper Junior, H.B. / Gorn, V.V. / Lukhtanov, E.A. / Foti, M. / West, J. / Meyer Junior, R.B. / Schweitzer, B.I.
CitationJournal: Nucleic Acids Res. / Year: 1998
Title: Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.
Authors: Kumar, S. / Reed, M.W. / Gamper Jr., H.B. / Gorn, V.V. / Lukhtanov, E.A. / Foti, M. / West, J. / Meyer Jr., R.B. / Schweitzer, B.I.
History
DepositionAug 29, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: 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 ...Database references / Derived calculations / Other / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
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(P*THXP*GP*AP*TP*TP*AP*TP*CP*TP*G)-3')
B: DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)6,7822
Polymers6,7822
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)1 / 6LEAST RESTRAINT VIOLATION
Representative

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Components

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


Mass: 3744.794 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER
#2: DNA chain DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3')


Mass: 3037.032 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A WITH A HEXAMETHYLENE LINKER

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Experimental details

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Experiment

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

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Sample preparation

Sample conditionspH: 6 / Temperature: 293.15 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLORBRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS, RELAXATION MATRIX REFINEMENT
Software ordinal: 1
Details: CANONICAL B-TYPE STRUCTURE USED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS GENERATING SIX STRUCTURES FROM DIFFERENT RANDOM NUMBER SEEDS. THE SIX STRUCTURES WERE SUBJECTED TO RELAXATION ...Details: CANONICAL B-TYPE STRUCTURE USED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS GENERATING SIX STRUCTURES FROM DIFFERENT RANDOM NUMBER SEEDS. THE SIX STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX REFINEMENT TO GENERATE THE SIX FINAL STRUCTURES. THESE SIX STRUCTURES WERE AVERAGED AND MINIMIZED TO GIVE THE FINAL STRUCTURE PRESENTED HERE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 6 / Conformers submitted total number: 1

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