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- PDB-1ql5: DNA DECAMER DUPLEX CONTAINING T5-T6 PHOTOADDUCT -

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Basic information

Entry
Database: PDB / ID: 1ql5
TitleDNA DECAMER DUPLEX CONTAINING T5-T6 PHOTOADDUCT
Components
  • DNA (5'-D(*CP*GP*CP*AP*TP*+TP*AP*CP*GP*C)- 3')
  • DNA (5'-D(*GP*CP*GP*TP*TP*AP*TP*GP*CP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DNA PHOTOPRODUCT / (6-4) ADDUCT / MUTAGENESIS
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, FULL RELAXATION MATRIX REFINEMENT
Model type detailsMINIMIZED AVERAGE
AuthorsLee, J.-H. / Hwang, G.-S. / Choi, B.-S.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: Solution Structure of a DNA Decamer Duplex Containing the 3' T.T Base Pair of the Cis-Syn Cyclobutane Pyrimidine Dimer: Implication for the Mutagenic Property of the Cis-Syn Dimer.
Authors: Lee, J.-H. / Choi, Y.-J. / Choi, B.-S.
History
DepositionAug 24, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references / Derived calculations / Version format compliance
Revision 1.2Jan 15, 2020Group: Derived calculations / Other / Category: pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_cs / _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 / _database_2.pdbx_database_accession

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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*TP*+TP*AP*CP*GP*C)- 3')
B: DNA (5'-D(*GP*CP*GP*TP*TP*AP*TP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,0852
Polymers6,0852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint5 kcal/mol
Surface area3620 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*TP*+TP*AP*CP*GP*C)- 3')


Mass: 3009.013 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CYCLOBUTANE RING FORMED BETWEEN C5-C6(T5) AND C5-C6(T6) DOUBLE BONDS
#2: DNA chain DNA (5'-D(*GP*CP*GP*TP*TP*AP*TP*GP*CP*G)-3')


Mass: 3076.015 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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

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: MISMATCHED BASE PAIRING OF 3'-T OF CIS-SYN DIMER WITH A RESIDUE. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 8 / Conformers submitted total number: 1

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