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- PDB-1zyf: Structure of a Supercoiling Responsive DNA Site -

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Entry
Database: PDB / ID: 1zyf
TitleStructure of a Supercoiling Responsive DNA Site
Components5'-D(*CP*AP*AP*CP*CP*AP*TP*GP*GP*TP*TP*G)-3'
KeywordsDNA / Supercoiling / Hix / recombinase / Hin
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics (XPLOR-NIH)
Model type detailsminimized average
AuthorsBae, S.H. / Yun, S.H. / Sun, D. / Lim, H.M. / Choi, B.S.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structural and dynamic basis of a supercoiling-responsive DNA element
Authors: Bae, S.H. / Yun, S.H. / Sun, D. / Lim, H.M. / Choi, B.S.
History
DepositionJun 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*AP*AP*CP*CP*AP*TP*GP*GP*TP*TP*G)-3'
B: 5'-D(*CP*AP*AP*CP*CP*AP*TP*GP*GP*TP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
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)26 / 100structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid-support Phosphoramidite Chemistry

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1322D TOCSY
1422D COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
110mM sodium phosphate (pH 6.8), 100mM NaCl90% H2O/10% D2O
210mM sodium phosphate (pH 6.8), 100mM NaCl100% D2O
Sample conditionsIonic strength: 10mM sodium phosphate, 100mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1995Bax, A.processing
MARDIGRAS3.2James, A.iterative matrix relaxation
VNMR3.1CVarian Inc.collection
X-PLORXPLOR-NIHBrungerstructure solution
X-PLORXPLOR-NIHrefinement
RefinementMethod: simulated annealing, torsion angle dynamics (XPLOR-NIH)
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 26

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