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- PDB-1iek: SOLUTION STRUCTURE OF THE DNA DUPLEX D(CCACCGGAAC).(GTTCCGGTGG) W... -

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Basic information

Entry
Database: PDB / ID: 1iek
TitleSOLUTION STRUCTURE OF THE DNA DUPLEX D(CCACCGGAAC).(GTTCCGGTGG) WITH A CHIRAL ALKYL-PHOSPHONATE MOIETY (DIAESTEREOISOMER S)
Components
  • 5'-D(*CP*CP*AP*CP*CP*(OCT)GP*GP*AP*AP*C)-3'
  • 5'-D(*GP*TP*TP*CP*CP*GP*GP*TP*GP*G)-3'
KeywordsDNA / double helix / dna bending / modified oligonucleotide / charge neutralization.
Function / homologyN-OCTANE / DNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics matrix relaxation
AuthorsSoliva, R. / Monaco, V. / Gomez-Pinto, I. / Meeuwenoord, N.J. / van der Marel, G.A. / van Boom, J.H. / Gonzalez, C. / Orozco, M.
CitationJournal: Nucleic Acids Res. / Year: 2001
Title: Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety.
Authors: Soliva, R. / Monaco, V. / Gomez-Pinto, I. / Meeuwenoord, N.J. / Marel, G.A. / Boom, J.H. / Gonzalez, C. / Orozco, M.
History
DepositionApr 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*CP*CP*(OCT)GP*GP*AP*AP*C)-3'
B: 5'-D(*GP*TP*TP*CP*CP*GP*GP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2053
Polymers6,0912
Non-polymers1141
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
Representative

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Components

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


Mass: 2998.983 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*TP*TP*CP*CP*GP*GP*TP*GP*G)-3'


Mass: 3092.013 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
232DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM duplex; 10mM phosphate, 100mM NaCl90% H20, 10% D2O
22mM duplex; 10mM phosphate, 100mM NaClD2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.0 1.0 atm5 K
27.0 1.0 atm25 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
MARDIGRAS5.2James, TLiterative matrix relaxation
Amber5Kollman, P.A.refinement
XwinNMR1.3Brukercollection
RefinementMethod: simulated annealing, molecular dynamics matrix relaxation
Software ordinal: 1
Details: the structures are based on a total of 271 NOE-derived distance constraints obtained from a complete relaxation matrix refinement. The structures were calculated by using restrained ...Details: the structures are based on a total of 271 NOE-derived distance constraints obtained from a complete relaxation matrix refinement. The structures were calculated by using restrained molecular dynamics with explicit solvent, and applying the particle mesh Ewald method.
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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