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- PDB-1ec4: SOLUTION STRUCTURE OF A HEXITOL NUCLEIC ACID DUPLEX WITH FOUR CON... -

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Basic information

Entry
Database: PDB / ID: 1ec4
TitleSOLUTION STRUCTURE OF A HEXITOL NUCLEIC ACID DUPLEX WITH FOUR CONSECUTIVE T:T BASE PAIRS
ComponentsHEXITOL DODECANUCLEOTIDE
KeywordsDNA / double helix / antisense / hexitol nucleic acid
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, and 'gentle' refinement
AuthorsLescrinier, E. / Esnouf, R.M. / Schraml, J. / Busson, R. / Herdewijn, P.
Citation
#1: Journal: J.Am.Chem.Soc. / Year: 1998
Title: Minor groove hydration contributes to the relative stability of HNA/RNA hybrids as compared to HNA/DNA complexes
Authors: De Winter, H. / Lescrinier, E. / Van Aerschot, A. / Herdewijn, P.
History
DepositionJan 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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: HEXITOL DODECANUCLEOTIDE
B: HEXITOL DODECANUCLEOTIDE


Theoretical massNumber of molelcules
Total (without water)7,6272
Polymers7,6272
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 / 100structures closest to the average of all refined structures
RepresentativeModel #1closest to the average

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Components

#1: DNA chain HEXITOL DODECANUCLEOTIDE


Mass: 3813.688 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE SUGAR MOIETIES ARE NOT DEOXYRIBOSE BUT D-ARABINO-HEXITOL

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131H,P-HETCOR
242WATERGATE NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM HNA; 0.3M NaClD2O
22mM HNA; 0.3M NaCl10% D2O, 90% H2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17ambient 293 K
27ambient 273 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.3variancollection
Felix97biosymdata analysis
X-PLOR3.851A.T. Brungerstructure solution
X-PLOR3.851A.T. Brungerrefinement
RefinementMethod: torsion angle dynamics, and 'gentle' refinement / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures closest to the average of all refined structures
Conformers calculated total number: 100 / Conformers submitted total number: 1

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