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- PDB-1n0k: NMR Structure of duplex DNA d(CCAAGGXCTTGGG), X is a 3' phosphogl... -

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Basic information

Entry
Database: PDB / ID: 1n0k
TitleNMR Structure of duplex DNA d(CCAAGGXCTTGGG), X is a 3' phosphoglycolate, 5'phosphate gapped lesion
Components
  • 5'-D(*CP*CP*AP*AP*GP*G)-3'
  • 5'-D(*CP*CP*CP*AP*AP*GP*GP*CP*CP*TP*TP*GP*G)-3'
  • 5'-D(P*CP*TP*TP*GP*GP*G)-3'
KeywordsDNA / bleomycin / phosphoglycolate
Function / homology2-PHOSPHOGLYCOLIC ACID / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / conjugate gradient
Model type detailsminimized average
AuthorsJunker, H.-D. / Hoehn, S.T. / Bunt, R.C. / Marathius, V. / Chen, J. / Turner, C.J. / Stubbe, J.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: Synthesis, Characterization and Solution Structure of Tethered Oligonucleotides Containing an Internal 3'-Phosphoglycolate, 5'-Phosphate Gapped Lesion
Authors: Junker, H.-D. / Hoehn, S.T. / Bunt, R.C. / Marathius, V. / Chen, J. / Turner, C.J. / Stubbe, J.
History
DepositionOct 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,7674
Polymers7,6113
Non-polymers1561
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 / 10minimum rmsd and nmr constraints violation
Representativeminimized average structure

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Components

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


Mass: 1818.231 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*CP*TP*TP*GP*GP*G)-3'


Mass: 1840.227 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*CP*CP*AP*AP*GP*GP*CP*CP*TP*TP*GP*G)-3'


Mass: 3952.574 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111PECOSY
121TOCSY
131NOESY
141HSQC
151GE-HSQC

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Sample preparation

DetailsContents: 1.4 mM oligonucleotide
Sample conditionsIonic strength: 40 mM NaH2PO4 / pH: 6.9 / Pressure: 1 atm / Temperature: 293.15 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
ModelField strength (MHz)Spectrometer-ID
custom build5001
custom build6002
custom build7503

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR3.851Brungerrefinement
XPLOR3.851Brungerstructure solution
RefinementMethod: conjugate gradient / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: minimum rmsd and nmr constraints violation
Conformers calculated total number: 10 / Conformers submitted total number: 1

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