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- PDB-2kh8: Solution Structure of cis-5R,6S-thymine glycol opposite complemen... -

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Basic information

Entry
Database: PDB / ID: 2kh8
TitleSolution Structure of cis-5R,6S-thymine glycol opposite complementary guanine in duplex DNA
Components
  • 5'-D(*AP*CP*AP*AP*AP*CP*GP*CP*GP*CP*AP*C)-3'
  • 5'-D(*GP*TP*GP*CP*GP*(CTG)P*GP*TP*TP*TP*GP*T)-3'
KeywordsDNA / Thymine Glycol
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsclosest to the average, model 1
AuthorsBrown, K.L.
CitationJournal: Biochemistry / Year: 2009
Title: The cis-(5R,6S)-thymine glycol lesion occupies the wobble position when mismatched with deoxyguanosine in DNA
Authors: Brown, K.L. / Basu, A.K. / Stone, M.P.
History
DepositionMar 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 22, 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(*GP*TP*GP*CP*GP*(CTG)P*GP*TP*TP*TP*GP*T)-3'
B: 5'-D(*AP*CP*AP*AP*AP*CP*GP*CP*GP*CP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3752
Polymers7,3752
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)10 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*GP*TP*GP*CP*GP*(CTG)P*GP*TP*TP*TP*GP*T)-3'


Mass: 3749.425 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*CP*AP*AP*AP*CP*GP*CP*GP*CP*AP*C)-3'


Mass: 3625.397 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: When base paired with guanine, the Thymine glycol equilibrium between cis-5R,6S-TG and trans-5R,6R-TG was not observed by NMR. In addition, the CTG can pucker so that the TG CH3 is in an ...Details: When base paired with guanine, the Thymine glycol equilibrium between cis-5R,6S-TG and trans-5R,6R-TG was not observed by NMR. In addition, the CTG can pucker so that the TG CH3 is in an axial or equatorial conformation. This entry is the cis-5R,6S-TG lesion opposite dG with TG CH3 in an equatorial conformation
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H COSY
2322D 1H-1H NOESY
1412D 31P-1H COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4, 100% D2O100% D2O
220 mM sodium phosphate-5, 100 mM sodium chloride-6, 10 uM sodium azide-7, 50 uM EDTA-8, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate-11
100 mMsodium chloride-21
10 uMsodium azide-31
50 uMEDTA-41
20 mMsodium phosphate-52
100 mMsodium chloride-62
10 uMsodium azide-72
50 uMEDTA-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.17ambient 303 K
20.17ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
TopSpinBruker Biospinprocessing
MARDIGRASBorgias, B.A. & James, T.L.restraint generation
CORMAJames T.L.structure validation
CurvesLavery, R. and Sklenar, Hdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing, molecular dynamics / 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: 10

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