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- PDB-1juu: NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution -

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Basic information

Entry
Database: PDB / ID: 1juu
TitleNMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution
Components
  • 5'-D(P*CP*CP*AP*TP*AP*AP*TP*TP*TP*AP*CP*C)-3'
  • 5'-D(P*CP*CP*TP*AP*TP*TP*AP*AP*AP*TP*CP*C)-3'
KeywordsDNA / Parallel stranded / DNA duplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsParvathy, V.R. / Bhaumik, S.R. / Chary, K.V.R. / Govil, G. / Liu, K. / Howard, F.B. / Miles, H.T.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: NMR structure of a parallel-stranded DNA duplex at atomic resolution.
Authors: Parvathy, V.R. / Bhaumik, S.R. / Chary, K.V. / Govil, G. / Liu, K. / Howard, F.B. / Miles, H.T.
History
DepositionAug 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: 5'-D(P*CP*CP*AP*TP*AP*AP*TP*TP*TP*AP*CP*C)-3'
B: 5'-D(P*CP*CP*TP*AP*TP*TP*AP*AP*AP*TP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,1632
Polymers7,1632
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)20 / 200structures with the lowest energy
RepresentativeModel #20fewest violations,lowest energy

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Components

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


Mass: 3581.368 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The DNA duplex was Synthesized with an Applied Biosystems Model 380B DNA synthesizer using solid state phosphoramidate chemistry
#2: DNA chain 5'-D(P*CP*CP*TP*AP*TP*TP*AP*AP*AP*TP*CP*C)-3'


Mass: 3581.368 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: COSY, NOESY, TOCSY
NMR detailsText: Structure was determined using 2D homonuclear experiments.

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Sample preparation

DetailsContents: 5 mM concentration of each dodecamer strand, 0.05 M deuterated sodium acetate buffer and 0.1 M NaCl
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 303 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 spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Discover3.1MSIstructure solution
Discover3.1MSIrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Structure was calculated using 78 nOe constraints, 28 hydrogen bond constraints, and 162 dihedral angle constraints.
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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