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- PDB-1snh: Solution structure of the DNA Decamer Duplex Containing Double TG... -

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Basic information

Entry
Database: PDB / ID: 1snh
TitleSolution structure of the DNA Decamer Duplex Containing Double TG Mismatches of Cis-syn Cyclobutane Pyrimidine Dimer
Components
  • 5'-D(*CP*GP*CP*AP*TP*TP*AP*CP*GP*C)-3'
  • 5'-D(*GP*CP*GP*TP*GP*GP*TP*GP*CP*G)-3'
KeywordsDNA / G-T mismatch / CPD / major groove widening
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsLee, J.H. / Park, C.J. / Shin, J.S. / Ikegami, T. / Akutsu, H. / Choi, B.S.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.
Authors: Lee, J.H. / Park, C.J. / Shin, J.S. / Ikegami, T. / Akutsu, H. / Choi, B.S.
History
DepositionMar 11, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,1222
Polymers6,1222
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)12 / 40structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #4fewest violations

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Components

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


Mass: 3004.981 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*GP*TP*GP*GP*TP*GP*CP*G)-3'


Mass: 3117.026 Da / Num. of mol.: 1 / 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 NOESY
2222D TOCSY
232DQF-COSY
2412D NOESY
352Natural Abundance 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl, 90% H2O, 10% D2090% H2O, 10% D20
21mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl, 100% D2O100% D2O
31mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl, 100% D2O, 15mg/ml Pf1100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NaCl 7ambient 274 K
2100mM NaCl 7ambient 290 K
3100mM NaCl 7ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
VNMR6.1Varian, Inc.collection
XPLOR-NIH2.9.4aG. Marius Clore , John Kuszewski, Charles D. Schwieters, and Nico Tjandrarefinement
X-PLOR3.1Brungerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a 500 NOE-derived distance constraints, 112 dihedral angle restraints, 13 residual dipolar coupling restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 12

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