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- PDB-3rec: ESCHERICHIA COLI RECA PROTEIN-BOUND DNA, NMR, 1 STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 3rec
TitleESCHERICHIA COLI RECA PROTEIN-BOUND DNA, NMR, 1 STRUCTURE
ComponentsDNA (5'-D(*TP*A)-3')
KeywordsDNA / DEOXYRIBOSE-BASE STACKING / HOMOLOGOUS RECOMBINATION / HOMOLOGOUS PAIRING / DEOXYRIBONUCLEIC ACID
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 17, 1997Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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*A)-3')


Theoretical massNumber of molelcules
Total (without water)5721
Polymers5721
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)1 / 100LEAST OVERALL ENERGY
Representative

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Components

#1: DNA chain DNA (5'-D(*TP*A)-3')


Mass: 572.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: D(TA) REGION OF D(TACG) RECA PROTEIN-BOUND DNA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: TRANSFERRED NOESY

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Sample preparation

Sample conditionspH: 7.1 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE MATERIAL AND METHODS SECTION OF THE ABOVE REFERENCE.
NMR ensembleConformer selection criteria: LEAST OVERALL ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 1

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