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- PDB-1jve: NMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop -

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Basic information

Entry
Database: PDB / ID: 1jve
TitleNMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop
ComponentsAT-Rich DNA with the GAA-Hairpin Loop
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DNA OLIGONUCLEOTIDE / STEM-AND-LOOP / AT-RICH / GAA HAIRPIN LOOP / PRIBNOW BOX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / full matrix relaxation analysis of NOE, random error analysis of NOE, simulated annealing using torsion angle dynamics, simulated annealing using Metropolis Monte Carlo, restrained minimization
AuthorsUlyanov, N.B. / Bauer, W.R. / James, T.L.
CitationJournal: J.Biomol.NMR / Year: 2002
Title: High-resolution NMR structure of an AT-rich DNA sequence.
Authors: Ulyanov, N.B. / Bauer, W.R. / James, T.L.
History
DepositionAug 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure viewerMolecule:
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Assembly

Deposited unit
A: AT-Rich DNA with the GAA-Hairpin Loop


Theoretical massNumber of molelcules
Total (without water)8,3221
Polymers8,3221
Non-polymers00
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 / 50Lowest target function (a weighted sum of conformational energy and restraint energy).
RepresentativeModel #1lowest energy

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Components

#1: DNA chain AT-Rich DNA with the GAA-Hairpin Loop


Mass: 8322.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Designed AT-rich sequence

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
121DQF-COSY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM DNA; phosphate buffer: 30 mM K+; 1mM EDTA / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 30 mM K+ / pH: 8.0 / Pressure: ambient / Temperature: 283 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 INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Associates, Inc.collection
NMRPipe1.8Delaglio, F.processing
Sparky3.1Goddard, T.D., Kneller, D.G.data analysis
MARDIGRAS3.2Borgias, B.A., Thomas, P.D., Liu, H., Kumar, A., Tonelli, M.iterative matrix relaxation
DYANA1.5Guntert, P.refinement
miniCarloalpha versionUlyanov, N.B., Gorler, A., Gorin, A.A., Zhurkin, V.B.refinement
RefinementMethod: full matrix relaxation analysis of NOE, random error analysis of NOE, simulated annealing using torsion angle dynamics, simulated annealing using Metropolis Monte Carlo, restrained minimization
Software ordinal: 1
Details: The NMR refinement was based on a total of 434 interproton distance restraints (16.1 per residue). The restraints include 353 MARDIGRAS-derived quantitative restraints for nonexchangeable ...Details: The NMR refinement was based on a total of 434 interproton distance restraints (16.1 per residue). The restraints include 353 MARDIGRAS-derived quantitative restraints for nonexchangeable protons (with an average flat-well width of 1.51 angstroms), 63 qualitative restraints for exchangeable protons, and 18 H-bond restraints for Watson-Crick GC pairs.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Lowest target function (a weighted sum of conformational energy and restraint energy).
Conformers calculated total number: 50 / Conformers submitted total number: 10

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