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- PDB-1k8l: XBY6: An analog of CK14 containing 6 dithiophosphate groups -

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Basic information

Entry
Database: PDB / ID: 1k8l
TitleXBY6: An analog of CK14 containing 6 dithiophosphate groups
Components
  • FIRST STRAND OF CK14 DNA DUPLEX
  • SECOND STRAND OF CK14 DNA DUPLEX
KeywordsDNA / XBY6 / CK14 / CK1 / PHOSPHORODITHIOATE / NF-KB
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model type detailsminimized average
AuthorsVolk, D.E. / Yang, X. / Fennewald, S.M. / King, D.J. / Bassett, S.E. / Venkitachalam, S. / Herzog, N. / Luxon, B.A. / Gorenstein, D.G.
CitationJournal: Bioorg.Chem. / Year: 2002
Title: Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB
Authors: Volk, D.E. / Yang, X. / Fennewald, S.M. / King, D.J. / Bassett, S.E. / Venkitachalam, S. / Herzog, N. / Luxon, B.A. / Gorenstein, D.G.
History
DepositionOct 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: 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: chem_comp / database_2 ...chem_comp / database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jun 22, 2022Group: Derived calculations / Category: pdbx_struct_mod_residue / Item: _pdbx_struct_mod_residue.parent_comp_id
Revision 1.5May 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: FIRST STRAND OF CK14 DNA DUPLEX
B: SECOND STRAND OF CK14 DNA DUPLEX


Theoretical massNumber of molelcules
Total (without water)8,7542
Polymers8,7542
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 / 10structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain FIRST STRAND OF CK14 DNA DUPLEX


Mass: 4314.044 Da / Num. of mol.: 1 / Fragment: DITHIOATED AT T10, C11 / Mutation: DITHIOATED AT T10, C11 / Source method: obtained synthetically
Details: SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY
#2: DNA chain SECOND STRAND OF CK14 DNA DUPLEX


Mass: 4440.326 Da / Num. of mol.: 1 / Fragment: DITHIOATED AT G17, C22, C24, G27 / Mutation: DITHIOATED AT G17, C22, C24, G27 / Source method: obtained synthetically
Details: SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
232DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. Proton resonances were assigned using COSY, TOCSY, and NOESY data

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM duplex, 12 mM Na2HPO4, 8 mM NaH2PO4, 56 mM NaCl, 50 uM NaN390% H2O/10% D2O
21 mM duplex, 12 mM Na2HPO4, 8 mM NaH2PO4, 56mM NaCl, 50 uM NaN399.96% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM 6.7ambient 278 K
2100 mM 6.7ambient 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
MORASS2.5Gorensteiniterative matrix relaxation
Amber5Case,Kollman, et alstructure solution
Amber5Case,Kollman, et alrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Distance restraints were derived by MORASS 2.5 using a total relaxation matrix approach. AMBER 5 was used for MD and minimization. The deposited structure represents the average of ten final structures
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 1

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