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- PDB-132d: SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX GCCGTTAACGGC CONTAININ... -

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Entry
Database: PDB / ID: 132d
TitleSOLUTION STRUCTURE OF THE TN AN DNA DUPLEX GCCGTTAACGGC CONTAINING THE HPA I RESTRICTION SITE
ComponentsDNA (5'-D(P*GP*CP*CP*GP*TP*TP*AP*AP*CP*GP*GP*C)-3')
KeywordsDNA / DOUBLE HELIX / HPA 1 RESTRICTION SITE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry
AuthorsKim, S.-G. / Reid, B.R.
CitationJournal: Biochemistry / Year: 1992
Title: Solution structure of the TnAn DNA duplex GCCGTTAACGCG containing the HpaI restriction site.
Authors: Kim, S.G. / Reid, B.R.
History
DepositionJun 24, 1993Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 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: 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(P*GP*CP*CP*GP*TP*TP*AP*AP*CP*GP*GP*C)-3')
B: DNA (5'-D(P*GP*CP*CP*GP*TP*TP*AP*AP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
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(P*GP*CP*CP*GP*TP*TP*AP*AP*CP*GP*GP*C)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized
Compound detailsTHE DNA DODECAMER CONTAINS THE HPA I RESTRICTION SEQUENCE D(GCCGTT:AACGGC)=2=.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: 2-D NMR SPECTRA WERE USED

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: DSPACE / Developer: Hare Research, Inc. / Classification: refinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: NOE DISTANCE CONSTRAINTS. THE R VALUE IS 0.18 FOR 80 INTERPROTON DISTANCES.
NMR ensembleConformers calculated total number: 1 / Conformers submitted total number: 1

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