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- PDB-169d: THE SOLUTION STRUCTURE OF THE R(GCG)D(TATACCC):D(GGGTATACGC) OKAZ... -

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Entry
Database: PDB / ID: 169d
TitleTHE SOLUTION STRUCTURE OF THE R(GCG)D(TATACCC):D(GGGTATACGC) OKAZAKI FRAGMENT CONTAINS TWO DISTINCT DUPLEX MORPHOLOGIES CONNECTED BY A JUNCTION
Components
  • DNA (5'-D(*GP*GP*GP*TP*AP*TP*AP*CP*GP*C)-3')
  • DNA/RNA (5'-R(*GP*CP*G)-D(P*TP*AP*TP*AP*CP*CP*C)-3')
KeywordsDNA-RNA HYBRID / DOUBLE HELIX / DNA/RNA HYBRID / DNA-RNA HYBRID complex
Function / homologyDNA / DNA/RNA hybrid
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsSalazar, M. / Fedoroff, O.Y. / Zhu, L. / Reid, B.R.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: The solution structure of the r(gcg)d(TATACCC):d(GGGTATACGC) Okazaki fragment contains two distinct duplex morphologies connected by a junction.
Authors: Salazar, M. / Fedoroff, O.Y.u. / Zhu, L. / Reid, B.R.
History
DepositionApr 11, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_keywords.text
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(*GP*GP*GP*TP*AP*TP*AP*CP*GP*C)-3')
B: DNA/RNA (5'-R(*GP*CP*G)-D(P*TP*AP*TP*AP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,1382
Polymers6,1382
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 / -
Representative

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Components

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


Mass: 3085.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#2: DNA/RNA hybrid DNA/RNA (5'-R(*GP*CP*G)-D(P*TP*AP*TP*AP*CP*CP*C)-3')


Mass: 3052.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: Discover / Developer: BIOSYM TECHNOLOGIES / Classification: refinement
RefinementMethod: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1
Details: FULL RELAXATION MATRIX SIMULATION OF THE TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT SPECTRA AT VARIOUS MIXING TIMES
NMR ensembleConformers submitted total number: 1

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