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- PDB-2l2u: NMR Solution Structures of +3 (5' staggered) Bistranded Abasic Si... -

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Basic information

Entry
Database: PDB / ID: 2l2u
TitleNMR Solution Structures of +3 (5' staggered) Bistranded Abasic Site Lesions in DNA
Components
  • DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3')
KeywordsDNA / Abasic Lesion / Bistranded DNA Lesions / Clustered DNA damage / Multiple DNA Damage / Ionizing Radiation
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics, DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsHazel, R.D. / de los Santos, C.
CitationJournal: Biochemistry / Year: 2010
Title: NMR solution structures of clustered abasic site lesions in DNA: structural differences between 3'-staggered (-3) and 5'-staggered (+3) bistranded lesions.
Authors: Hazel, R.D. / de los Santos, C.
History
DepositionAug 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3')
B: DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)8,3122
Polymers8,3122
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)4 / 20structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 4180.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#2: DNA chain DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3')


Mass: 4131.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide

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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
1312D DQF-COSY
1412D 1H-1H TOCSY

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Sample preparation

DetailsContents: unknown mM DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3'), unknown mM DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3'), 100% D2O
Solvent system: 100% D2O
Sample
UnitsComponentSolution-ID
mMDNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3')-11
mMDNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3')-21
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungergeometry optimization
X-PLOR3.1Brungerrefinement
RefinementMethod: molecular dynamics, DGSA-distance geometry simulated annealing
Software ordinal: 1
Details: Authors indicate chirality error at DT8 in model 1 due to flexibility of the DNA duplex in solution
NMR constraintsNOE constraints total: 554
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 4

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