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- PDB-1ew1: RECA PROTEIN-BOUND SINGLE-STRANDED DNA -

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Basic information

Entry
Database: PDB / ID: 1ew1
TitleRECA PROTEIN-BOUND SINGLE-STRANDED DNA
ComponentsDNA (5'-D(*TP*AP*CP*G)-3')
KeywordsDNA / DEOXYRIBOSE-BASE STACKING / SINGLE-STRANDED DNA
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsNishinaka, T. / Ito, Y. / Yokoyama, S. / Shibata, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: An extended DNA structure through deoxyribose-base stacking induced by RecA protein.
Authors: Nishinaka, T. / Ito, Y. / Yokoyama, S. / Shibata, T.
History
DepositionApr 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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 visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RECA PROTEIN-BOUND SINGLE-STRANDED DNA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using transferred NOE techniques. THE ROOT-MEAN-SQUARE DEVIATION OF THE T-A-C REGION IS 0.30 ANGSTROM. THE FOURTH RESIDUE (G) IS DISORDERED BECAUSE OF FEW NOE CONSTRAINTS

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Sample preparation

DetailsContents: 0.8mM d(TpApCpG); 20mM Tris-Cl, 6.7mM MgCl2, 150mM NaCl
Solvent system: D2O
Sample conditionsIonic strength: 6.7mM MgCl2, 150mM NaCl / pH: 7.1 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
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

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