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- PDB-149d: SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA... -

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Basic information

Entry
Database: PDB / ID: 149d
TitleSOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA TRIPLEX CONTAINING T(DOT)AT, C+(DOT)GC AND G(DOT)TA TRIPLES
Components
  • 5'-D(*CP*CP*TP*AP*TP*TP*C)-3'
  • 5'-D(*CP*TP*TP*GP*TP*CP*C)-3'
  • 5'-D(*GP*AP*AP*TP*AP*GP*G)-3'
KeywordsDNA / TRIPLEX
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR
AuthorsRadhakrishnan, I. / Patel, D.J.
Citation
Journal: Structure / Year: 1994
Title: Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples.
Authors: Radhakrishnan, I. / Patel, D.J.
#1: Journal: Biochemistry / Year: 1992
Title: Three-Dimensional Homonuclear Noesy-Tocsy of an Intramolecular Pyrimidine(Dot)Purine(Dot)Pyrimidine DNA Triplex Containing a Central G(Dot)Ta Triple: Nonexchangeable Proton Assignments and Structural Implications
Authors: Radhakrishnan, I. / Patel, D.J. / Gao, X.
#2: Journal: J.Am.Chem.Soc. / Year: 1992
Title: Solution Conformation of a G(Dot)Ta Triple in an Intramolecular Pyrimidine(Dot)Purine(Dot)Pyrimidine DNA Triplex
Authors: Radhakrishnan, I. / Patel, D.J. / Veal, J.M. / Gao, X.
#3: Journal: Biochemistry / Year: 1991
Title: NMR Structural Studies of Intramolecular (Y+)N(Dot)(R+)N(Y-)N DNA Triplexes in Solution: Imino and Amino Proton and Nitrogen Markers of G(Dot)Ta Base Triple Formation
Authors: Radhakrishnan, I. / Gao, X. / De Los Santos, C. / Live, D. / Patel, D.J.
History
DepositionNov 15, 1993Processing site: BNL
Revision 1.0Apr 30, 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,2993
Polymers6,2993
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: THREE RESIDUES IN THE SEQUENCE STUDIED ARE CYTOSINES THAT ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES DIFFER FROM "NORMAL" CYTOSINES IN THAT THEY HAVE A PROTON ATTACHED TO THE N3 NITROGEN. ...1: THREE RESIDUES IN THE SEQUENCE STUDIED ARE CYTOSINES THAT ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES DIFFER FROM "NORMAL" CYTOSINES IN THAT THEY HAVE A PROTON ATTACHED TO THE N3 NITROGEN. IT SHOULD BE NOTED THAT THIS IS NOT A PERMANENT MODIFICATION BUT RATHER A CONSEQUENCE OF THE CONDITIONS UNDER WHICH THE SEQUENCE WAS STUDIED. THESE N3-PROTONATED CYTOSINE RESIDUES HAVE BEEN ASSIGNED THE RESIDUE NAME C IN THE ENTRY AND ATOM H3 HAS BEEN FOOTNOTED.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / -
Representative

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Components

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


Mass: 2048.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#2: DNA chain 5'-D(*GP*AP*AP*TP*AP*GP*G)-3'


Mass: 2186.473 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*TP*TP*GP*TP*CP*C)-3'


Mass: 2064.372 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: R VALUE 0.022 RMSD BOND DISTANCES 0.005 ANGSTROMS RMSD BOND ANGLES 2.26 DEGREES
NMR ensembleConformers submitted total number: 14

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