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- PDB-1qkg: DNA DECAMER DUPLEX CONTAINING T-T DEWAR PHOTOPRODUCT -

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Basic information

Entry
Database: PDB / ID: 1qkg
TitleDNA DECAMER DUPLEX CONTAINING T-T DEWAR PHOTOPRODUCT
Components
  • DNA (5'-D(*CP*GP*CP*AP*(HYD)TP*+TP*AP*CP*GP*C)-3')
  • DNA (5'-D(*GP*CP*GP*TP*GP*AP*TP*GP*CP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DNA PHOTOPRODUCT / DEWAR PRODUCT / (6-4) ADDUCT / MUTAGENESIS / TRANSLESION REPLICATION
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, FULL RELAXATION MATRIX REFINEMENT
Model type detailsMINIMIZED AVERAGE
AuthorsLee, J.-H. / Bae, S.-H. / Choi, Y.-J. / Choi, B.-S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Dewar Photoproduct of Thymidylyl(3'-->5')-Thymidine (Dewar Product) Exhibits Mutagenic Behavior in Accordance with the "A Rule".
Authors: Lee, J.-H. / Bae, S.-H. / Choi, B.-S.
History
DepositionJul 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Derived calculations / Other / Category: pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Jun 19, 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(*CP*GP*CP*AP*(HYD)TP*+TP*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*GP*AP*TP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,1102
Polymers6,1102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint2 kcal/mol
Surface area3760 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 8LEAST RESTRAINT VIOLATION
Representative

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Components

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


Mass: 3009.014 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: BOND FORMED BETWEEN C6(T5) AND C4(T6) BOND FORMED BETWEEN N3(T6) AND C6(T6)
#2: DNA chain DNA (5'-D(*GP*CP*GP*TP*GP*AP*TP*GP*CP*G)-3')


Mass: 3101.028 Da / Num. of mol.: 1 / Source method: obtained synthetically
Compound detailsMISMATCHED BASE PAIRING OF 3'-T OF DEWAR PRODUCT WITH G RESIDUE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY
NMR detailsText: MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING SA METHOD WITH DISTANCE RESTRAINTS AND FULL RELAXATION MATRIX REFINEMENT WITH NOE INTENSITY RESTRAINTS OF 50, 80, 160 MS MIXING TIMES

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Sample preparation

DetailsContents: 100% D2O, 10% WATER/90% D2O
Sample conditionspH: 6.6 / Temperature: 274.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, FULL RELAXATION MATRIX REFINEMENT
Software ordinal: 1
Details: RESTRAINED MOLECULAR DYNAMICS WITH NMR-DERIVEN DISTANCE RESTRAINTS AND THEN FULL RELAXATION MATRIX REFINEMENT WITH NOE VOLUME ITENSITY RESTRAINTS
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 8 / Conformers submitted total number: 1

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