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- PDB-124d: STRUCTURE OF A DNA:RNA HYBRID DUPLEX: WHY RNASE H DOES NOT CLEAVE... -

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Basic information

Entry
Database: PDB / ID: 124d
TitleSTRUCTURE OF A DNA:RNA HYBRID DUPLEX: WHY RNASE H DOES NOT CLEAVE PURE RNA
Components
  • DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*G)-3')
  • RNA (5'-R(*CP*AP*UP*GP*UP*GP*AP*C)-3')
KeywordsDNA-RNA HYBRID / DNA-RNA COMPLEX / DOUBLE HELIX
Function / homologyDNA / RNA
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, NOESY SIMULATION REFINEMENT
AuthorsFedoroff, O.Y. / Salazar, M. / Reid, B.R.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Structure of a DNA:RNA Hybrid Duplex. Why Rnase H Does not Cleave Pure RNA
Authors: Fedoroff, O.Y. / Salazar, M. / Reid, B.R.
#1: Journal: Biochemistry / Year: 1993
Title: The DNA Strand in DNA-RNA Hybrid Duplexes is Neither B-Form Nor A-Form in Solution
Authors: Salazar, M. / Fedoroff, O.Y. / Miller, J.M. / Ribeiro, N.S. / Reid, B.R.
History
DepositionMay 7, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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: 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(*GP*TP*CP*AP*CP*AP*TP*G)-3')
B: RNA (5'-R(*CP*AP*UP*GP*UP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,9532
Polymers4,9532
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 / 1
Representative

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Components

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


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#2: RNA chain RNA (5'-R(*CP*AP*UP*GP*UP*GP*AP*C)-3')


Mass: 2526.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYHTHESIZED

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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

RefinementMethod: RESTRAINED MOLECULAR DYNAMICS, NOESY SIMULATION REFINEMENT
Software ordinal: 1
Details: 132 NOE RESTRAINTS AND 20 HYDROGEN BONDS WERE USED.
NMR ensembleConformers calculated total number: 1 / Conformers submitted total number: 1

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