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- PDB-1naj: High resolution NMR Structure Of DNA Dodecamer Determined In Aque... -

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Basic information

Entry
Database: PDB / ID: 1naj
TitleHigh resolution NMR Structure Of DNA Dodecamer Determined In Aqueous Dilute Liquid Crystalline Phase
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / Dickerson Dodecamer
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
AuthorsWu, Z. / Delaglio, F. / Tjandra, N. / Zhurkin, V. / Bax, A.
CitationJournal: J.Biomol.Nmr / Year: 2003
Title: Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and (31)P chemical shift anisotropy.
Authors: Wu, Z. / Delaglio, F. / Tjandra, N. / Zhurkin, V.B. / Bax, A.
History
DepositionNov 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
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)5 / 20structures with the lowest energy
RepresentativeModel #3lowest energy

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111H-31P-HSQC, HP-ctNOESY-DIF, COSY
122COSY,2D NOESY,13C-HSQC-J-MODULATED,13C-HSQC-F1-COUPLED, 15N-HSQC-F1-COUPLED

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 MM unlabeled DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0100% D2O
20.5 MM U-13C/15N DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.090% H2O/10% D2O
Sample conditionsIonic strength: 40mM / pH: 7 / Pressure: 1 atm / Temperature: 308 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
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7 REV 1999.039.11.31Delaglio, Frankdata analysis
XwinNMRVERSION 2.4 and 2.6Brukercollection
X-PLOR3.841BRUNGERrefinement
CosyViewDelaglio, Frankdata analysis
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 32 HYDROGEN BOND, AND 24 DIHEDRAL RESTRAINTS; AS WELL AS 262 CH AND 16 NH ONE-BOND DIPOLAR COUPLING RESTRAINTS, 200 APPROXIMATE PROTON-PROTON ...Details: THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 32 HYDROGEN BOND, AND 24 DIHEDRAL RESTRAINTS; AS WELL AS 262 CH AND 16 NH ONE-BOND DIPOLAR COUPLING RESTRAINTS, 200 APPROXIMATE PROTON-PROTON DIPOLAR COUPLINGS, 300 quantitative proton-proton dipolar restraints, 22 31P-1H dipolar couplings, and 22 31P chemical shift anisotropy restraints. THE COORDINATE OF THE ALIGNMENT TENSOR IS DEFINED BY molecule 500 and 501.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 5

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