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- PDB-1gj0: NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: BE... -

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Basic information

Entry
Database: PDB / ID: 1gj0
TitleNMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: BETA ANOMER
Components
  • 5'-D(*CP*CP*AP*AP*AP*GP*(AAB)P*AP*CP*TP*GP*GP*G)-3'
  • 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'
KeywordsDNA / DAMAGED DNA / APYRIMIDINIC SITE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsHoehn, S.T. / Turner, C.J. / Stubbe, J.
CitationJournal: Nucleic Acids Res. / Year: 2001
Title: Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation.
Authors: Hoehn, S.T. / Turner, C.J. / Stubbe, J.
History
DepositionOct 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 1.4Dec 27, 2023Group: 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*CP*AP*AP*AP*GP*(AAB)P*AP*CP*TP*GP*GP*G)-3'
B: 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,8352
Polymers7,8352
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*CP*AP*AP*AP*GP*(AAB)P*AP*CP*TP*GP*GP*G)-3'


Mass: 3892.526 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'


Mass: 3942.572 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
121PE-COSY
232WATERGATE-NOESY
34331P-HCOSY
35331P-decoupled-PE-COSY
36331P-decoupled-J-scaled-DQCOSY
NMR detailsText: THE ABASIC SITE DEOXYRIBOSE 1H-1H COUPLING CONSTANTS AND THE DNA 31P-H3' COUPLING CONSTANTS WERE EXPERIMENTALLY DETERMINED. THIS INFORMATION WAS USED IN THE MODELING PROTOCOL.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate bufferD2O
22.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer10% D2O, 90% H2O
33 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate bufferD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM sodium phosphate buffer 6.8 ambient 293 K
210 mM sodium phosphate buffer 6.8 ambient 278 K
310 mM sodium phosphate buffer 6.8 ambient 298 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
Home-built HOME BUILTHome-builtHOME BUILT7501
Home-built HOME BUILTHome-builtHOME BUILT6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
Felix95MSIprocessing
Felix95MSIdata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: THE STRUCTURE IS BASED ON 475 NOE-DERIVED DISTANCE CONSTRAINTS AND 101 DIHEDRAL ANGLE RESTRAINTS.
NMR ensembleConformers submitted total number: 1

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