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- PDB-2lg3: Structure of the duplex containing HNE derived (6S,8R,11S) gamma-... -

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Basic information

Entry
Database: PDB / ID: 2lg3
TitleStructure of the duplex containing HNE derived (6S,8R,11S) gamma-HO-PdG when placed opposite dT
Components
  • DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3')
KeywordsDNA / trans-4-hydroxynonenal / gamma-HO-PdG
Function / homology(4S)-nonane-1,4-diol / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsHuang, H. / Wang, H. / Kozekova, A. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P.
CitationJournal: To be Published
Title: Ring-chain tautomerization of trans-4-hydroxynonenal derived (6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct when placed opposite 2'-deoxythymidine in duplex
Authors: Huang, H. / Wang, H. / Kozekova, A. / Lloyd, R.S. / Rizzo, C.J. / Stone, M.P.
History
DepositionJul 19, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 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*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5023
Polymers7,3422
Non-polymers1601
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 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

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


Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3')


Mass: 3678.403 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-HND / (4S)-nonane-1,4-diol


Mass: 160.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'), 1 mM DNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3'), 1 mM (2E,4R)-4-HYDROXYNON-2-ENAL, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMDNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')-11
1 mMDNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3')-21
1 mM(2E,4R)-4-HYDROXYNON-2-ENAL-31
Sample conditionsIonic strength: 100 / 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 softwareName: Amber
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 1

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