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- PDB-1kr8: Refinement of d(GCGAAGC) Hairpin Structure Using One-and Two-Bond... -

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Basic information

Entry
Database: PDB / ID: 1kr8
TitleRefinement of d(GCGAAGC) Hairpin Structure Using One-and Two-Bonds Residual Dipolar Couplings
Components5'-D(*GP*CP*GP*AP*AP*GP*C)-3'
KeywordsDNA / hairpin / GA mismatch
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsPadrta, P. / Stefl, R. / Zidek, L. / Sklenar, V.
CitationJournal: J.BIOMOL.NMR / Year: 2002
Title: Refinement of d(GCGAAGC) Hairpin Structure Using One- and Two-Bond Residual Dipolar Couplings
Authors: Padrta, P. / Stefl, R. / Kralik, L. / Zidek, L. / Sklenar, V.
History
DepositionJan 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 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_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(*GP*CP*GP*AP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)2,1471
Polymers2,1471
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)14 / 14all calculated structures submitted
RepresentativeModel #7closest to the average

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Components

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


Mass: 2147.437 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in replication origins of phage phiX174, in herpes simplex virus, in E. coli heat-shock gene and rRNA genes.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
131E-COSY
141DQF-COSY
353coupled HSQC
363S3E E-COSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy in isotropic and liquid crystalline phase.

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Sample preparation

Details
Solution-IDContentsSolvent system
16mM natural abundance d(GCGAAGC), 10mM phosphate buffer Na, D2OD2O
26mM natural abundance d(GCGAAGC), 10mM phosphate buffer Na, 90% H2O, 10% D2O90% H2O/10% D2O
3U-15N,13C, 0.5mM d(GCGAAGC), 10mM phosphate buffer Na, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM 6.71 atm303 K
210 mM 6.71 atm277 K
310 mM 6.71 atm303 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1, 3.0Brukercollection
XwinNMR2.1, 3.0Brukerprocessing
Sparky3.xT. D. Goddard and D. G. Knellerdata analysis
Amber6Kollman, Case et. alstructure solution
Amber6Kollman, Case et. alrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 14 / Conformers submitted total number: 14

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