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- PDB-2lia: Solution NMR structure of a DNA dodecamer containing the 7-aminom... -

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Basic information

Entry
Database: PDB / ID: 2lia
TitleSolution NMR structure of a DNA dodecamer containing the 7-aminomethyl-7-deaza-2'-deoxyguanosine adduct
ComponentsDNA (5'-D(*GP*AP*GP*AP*(2LA)P*CP*GP*CP*TP*CP*TP*C)-3')
KeywordsDNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsSzulik, M.W. / Ganguly, M. / Wang, R. / Gold, B. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2013
Title: Site-Specific Stabilization of DNA by a Tethered Major Groove Amine, 7-Aminomethyl-7-deaza-2'-deoxyguanosine.
Authors: Szulik, M.W. / Voehler, M.W. / Ganguly, M. / Gold, B. / Stone, M.P.
History
DepositionAug 26, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: 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_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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*(2LA)P*CP*GP*CP*TP*CP*TP*C)-3')
B: DNA (5'-D(*GP*AP*GP*AP*(2LA)P*CP*GP*CP*TP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,3832
Polymers7,3832
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 / 42back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*AP*(2LA)P*CP*GP*CP*TP*CP*TP*C)-3')


Mass: 3691.445 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
1212D 1H-1H COSY

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Sample preparation

DetailsContents: 0.25 mM [U-2H] DNA dodecamer, 10 mM [U-2H] sodium phosphate, 200 mM [U-2H] sodium chloride, 0.011 M [U-2H] sodium azide, 0.05 mM [U-2H] sodium EDTA, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.25 mMDNA dodecamer-1[U-2H]1
10 mMsodium phosphate-2[U-2H]1
200 mMsodium chloride-3[U-2H]1
0.011 Msodium azide-4[U-2H]1
0.05 mMsodium EDTA-5[U-2H]1
Sample conditionsIonic strength: 0.21 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.0.b.6Bruker Biospinprocessing
SparkyGoddardchemical shift assignment
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 211 / NOE intraresidue total count: 114 / NOE sequential total count: 97
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 42 / Conformers submitted total number: 1
NMR ensemble rmsDistance rms dev: 0.453 Å

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