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- PDB-156d: REFINED SOLUTION STRUCTURE OF THE DIMERIC QUADRUPLEX FORMED FROM ... -

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Entry
Database: PDB / ID: 156d
TitleREFINED SOLUTION STRUCTURE OF THE DIMERIC QUADRUPLEX FORMED FROM THE OXYTRICHA TELOMERIC OLIGONUCLEOTIDE D(GGGGTTTTGGGG)
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
KeywordsDNA / QUADRUPLEX / OXYTRICHA TELOMERIC OLIGONUCLEOTIDE D(GGGGTTTTGGGG)
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / SUBSTRUCTURE EMBEDDING, SIMULATED ANNEALING, MATRIX RELAXATION
Model type detailsminimized average
AuthorsSchultze, P. / Smith, F.W. / Feigon, J.
Citation
Journal: Structure / Year: 1994
Title: Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG).
Authors: Schultze, P. / Smith, F.W. / Feigon, J.
#1: Journal: Biochemistry / Year: 1993
Title: Strand Orientation in the DNA Quadruplex Formed from the Oxytricha Telomere Repeat Oligonucleotide D(G4T4G4) in Solution
Authors: Smith, F.W. / Feigon, J.
#2: Journal: Nature / Year: 1992
Title: Quadruplex Structure of Oxytricha Telomeric DNA Oligonucleotides
Authors: Smith, F.W. / Feigon, J.
History
DepositionJan 17, 1994Processing 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 (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
B: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,6112
Polymers7,6112
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)8 / 20structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3805.460 Da / Num. of mol.: 2 / 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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Sample preparation

DetailsSolvent system: H2O/D20
SampleConc.: 0.0052 M / Component: SODIUM CHLORIDE
Sample conditionsIonic strength: .05M / pH: 6.0 / Temperature units: K
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
RefinementMethod: SUBSTRUCTURE EMBEDDING, SIMULATED ANNEALING, MATRIX RELAXATION
Software ordinal: 1
Details: REFINEMENT PROCEDURE STEP (1) SUBSTRUCTURE EMBEDDING ON 20 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY SIMULATED ANNEALING (20 STRUCTURES) STEP (3) SIMULATED ANNEALING AND ...Details: REFINEMENT PROCEDURE STEP (1) SUBSTRUCTURE EMBEDDING ON 20 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY SIMULATED ANNEALING (20 STRUCTURES) STEP (3) SIMULATED ANNEALING AND ENERGY MINIMIZATION (20 STRUCTURES) STEP (4) RELAXATION MATRIX REFINEMENT ON THE BEST 8 OF 20 STRUCTURES. THE DIMER POSSESSES A TWO-FOLD AXIS OF SYMMETRY. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 1 WHEN APPLIED TO CHAIN A OF MODEL 1. THE COORDINATES OF THE ATOMS OF CHAIN A TRANSFORMED IN THIS MANNER HAVE AN RMSD OF 0.0015 ANGSTROMS FROM THE COORDINATES OF CHAIN B GIVEN IN THIS ENTRY.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 8

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