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- PDB-2rpd: Mhr1p-bound ssDNA -

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Basic information

Entry
Database: PDB / ID: 2rpd
TitleMhr1p-bound ssDNA
ComponentsDNA (5'-D(*DTP*DAP*DCP*DG)-3')
KeywordsDNA / ssDNA / Mhr1 / RecA
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsMasuda, T. / Ito, Y. / Shibata, T. / Mikawa, T.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: A non-canonical DNA structure enables homologous recombination in various genetic systems
Authors: Masuda, T. / Ito, Y. / Terada, T. / Shibata, T. / Mikawa, T.
History
DepositionMay 15, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 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: DNA (5'-D(*DTP*DAP*DCP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)1,1911
Polymers1,1911
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*DTP*DAP*DCP*DG)-3')


Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.5mM DNA, 100% D2O / Solvent system: 100% D2O
SampleConc.: 0.5 mM / Component: DNA
Sample conditionsIonic strength: 50 / pH: 7.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Cloreprocessing
X-PLOR NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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