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- PDB-135d: SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIP... -

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Basic information

Entry
Database: PDB / ID: 135d
TitleSOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES
ComponentsDNA TRIPLEX
KeywordsDNA / TRIPLEX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY
AuthorsRadhakrishnan, I. / Patel, D.J.
Citation
Journal: Structure / Year: 1993
Title: Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples.
Authors: Radhakrishnan, I. / Patel, D.J.
#1: Journal: J.Am.Chem.Soc. / Year: 1993
Title: Solution Structure of an Intramolecular Purine(Dot)Purine(Dot)Pyrimidine DNA Triplex
Authors: Radhakrishnan, I. / Patel, D.J.
History
DepositionAug 30, 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

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Assembly

Deposited unit
A: DNA TRIPLEX


Theoretical massNumber of molelcules
Total (without water)9,5521
Polymers9,5521
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 TRIPLEX


Mass: 9552.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY / Software ordinal: 1
Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ONIDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE ...Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ONIDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045.
NMR ensembleConformers submitted total number: 1
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_d3.959
X-RAY DIFFRACTIONx_improper_angle_d0.433

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