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- PDB-2lwg: NMR Structure of the Self-Complementary 10 mer DNA Oligonucleotid... -

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Basic information

Entry
Database: PDB / ID: 2lwg
TitleNMR Structure of the Self-Complementary 10 mer DNA Oligonucleotide 5'-GGATATATCC-3'.
ComponentsDNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')
KeywordsDNA / DNA microstructure / Induced DNA binding / DNA minor groove variations
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsRettig, M. / Germann, M.W. / Wilson, W. / Wang, S.
CitationJournal: Chembiochem / Year: 2013
Title: Molecular basis for sequence-dependent induced DNA bending.
Authors: Rettig, M. / Germann, M.W. / Wang, S. / Wilson, W.D.
History
DepositionJul 31, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')
2: DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,0882
Polymers6,0882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area425.6 Å2
ΔGint-5.6 kcal/mol
Surface area2369.28 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 5000target function
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3044.017 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1312D DQF-COSY
1432D 1H-1H NOESY
1532D 1H-13C HSQC aliphatic
1632D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3'), 100% D2O100% D2O
20.9 mM DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3'), 90% H2O/10% D2O90% H2O/10% D2O
31.2 mM DNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3'), 11 mg/mL Pf1 phage, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.9 mMDNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')-11
0.9 mMDNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')-22
1.2 mMDNA (5'-D(*GP*GP*AP*TP*AP*TP*AP*TP*CP*C)-3')-33
11 mg/mLPf1 phage-43
Sample conditionspH: 7 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 5000 / Conformers submitted total number: 11

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