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- PDB-1pqt: REFINEMENT OF d(GCGAAGC) HAIRPIN STRUCTURE USING ONE- AND TWO-BON... -

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Entry
Database: PDB / ID: 1pqt
TitleREFINEMENT OF d(GCGAAGC) HAIRPIN STRUCTURE USING ONE- AND TWO-BOND 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
DepositionJun 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 #7

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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
121E-COSY
131DQF-COSY
141COUPLED HSQC
151S3E 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

DetailsContents: 6MM NATURAL ABUNDANCE D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, D2O; 6MM NATURAL ABUNDANCE D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, 90% H2O, 10% D2O; U-15N,13C, 0.5MM D(GCGAAGC), 10MM PHOSPHATE ...Contents: 6MM NATURAL ABUNDANCE D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, D2O; 6MM NATURAL ABUNDANCE D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, 90% H2O, 10% D2O; U-15N,13C, 0.5MM D(GCGAAGC), 10MM PHOSPHATE BUFFER NA, 90% H2O, 10% D2O
Sample conditionsIonic strength: 10 mM / pH: 6.7 / Pressure: 1 atm / 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: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber7KOLLMAN, CASE ET. ALrefinement
XwinNMR2.1Brukercollection
XwinNMR3Brukercollection
Sparky3.XT. D. Goddard and D. G. Knellerdata analysis
Amber7KOLLMAN, CASE ET. ALstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 14 / Conformers submitted total number: 14

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