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- PDB-1kbm: SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANI... -

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Basic information

Entry
Database: PDB / ID: 1kbm
TitleSOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE OPPOSITE THYMINE
Components
  • 5'-D(*CP*GP*TP*AP*CP*(S6G)P*CP*AP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3'
KeywordsDNA / THIOGUANINE / 6-THIOGUANINE / TG / 6TG / S6G / THIOPURINE / DOUBLE HELIX / B-FORM DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS SIMULATIONS
AuthorsBohon, J. / De Los Santos, C.R.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: Structural effect of the anticancer agent 6-thioguanine on duplex DNA.
Authors: Bohon, J. / de los Santos, C.R.
History
DepositionNov 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 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(*CP*GP*TP*AP*CP*(S6G)P*CP*AP*TP*GP*C)-3'
B: 5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,7392
Polymers6,7392
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)1 / -
Representative

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Components

#1: DNA chain 5'-D(*CP*GP*TP*AP*CP*(S6G)P*CP*AP*TP*GP*C)-3'


Mass: 3350.252 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3'


Mass: 3389.221 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
111NOESY
121COSY
131DQFCOSY
141COSY45
151TOCSY
161HETCO
272NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED BY THE FULL-RELAXATION MATRIX BACK-CALCULATION METHOD. 15 ...Text: THE STRUCTURE WAS DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED BY THE FULL-RELAXATION MATRIX BACK-CALCULATION METHOD. 15 STRUCTURES EACH WERE DETERMINED FROM A- AND B-FORM DNA STARTING STRUCTURES. FIVE DIFFERENT STARTING TEMPERATURES AND THREE DIFFERENT LENGTHS OF TIME SPENT AT THE HIGH-TEMPERATURE STEP MAKE UP THE 15 STRUCTURES. 29 OF THE 30 TOTAL STRUCTURES CONVERGED TO AN RMSD OF .52A OR LESS. THE AVERAGE OF THESE 29 STRUCTURES WAS CALCULATED AND UTILIZED IN THE FULL RELAXATION MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM THIS LAST STEP IS THE FORM THAT IS DEPOSITED HERE.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM DNA, 25mM PHOSPHATE Buffer, 50mM NaCl, 0.5mM EDTA100% D2O
22mM DNA, 25mM PHOSPHATE Buffer, 50mM NaCl, 0.5mM EDTA10 % D2O, 90 % H20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA 6.78AMBIENT 298 K
225mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA 6.78AMBIENT 276 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Felix95 AND 98BIOSYM TECHNOLOGIES, INC.processing
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS SIMULATIONS / Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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