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- PDB-230d: SOLUTION STRUCTURES OF UNIMOLECULAR QUADRUPLEXES FORMED BY OLIGON... -

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Entry
Database: PDB / ID: 230d
TitleSOLUTION STRUCTURES OF UNIMOLECULAR QUADRUPLEXES FORMED BY OLIGONUCLEOTIDES CONTAINING OXYTRICHA TELOMERE REPEATS
ComponentsQUADRUPLEXES DNA
KeywordsDNA / QUADRUPLEX / OXYTRICHA TELOMERE REPEAT
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, MATRIX RELAXATION
AuthorsSmith, F.W. / Schultze, P. / Feigon, J.
Citation
Journal: Structure / Year: 1995
Title: Solution structures of unimolecular quadruplexes formed by oligonucleotides containing Oxytricha telomere repeats.
Authors: Smith, F.W. / Schultze, P. / Feigon, J.
#1: Journal: Nature / Year: 1992
Title: Quadruplex Structure of Oxytricha Telomeric DNA Oligonucleotides
Authors: Smith, F.W. / Feigon, J.
History
DepositionAug 24, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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: QUADRUPLEXES DNA


Theoretical massNumber of molelcules
Total (without water)8,8021
Polymers8,8021
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)7 / 80structures with the lowest energy
Representative

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Components

#1: DNA chain QUADRUPLEXES DNA


Mass: 8801.531 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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Sample preparation

DetailsSolvent system: H2O/D2O
SampleConc.: 0.002 M / Component: SODIUM CHLORIDE
Sample conditionsIonic strength: 0.1M / pH: 6 / Temperature units: K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementMethod: SIMULATED ANNEALING, MATRIX RELAXATION / Software ordinal: 1
Details: REFINEMENT PROCEDURE STEP (1) SUBSTRUCTURE EMBEDDING ON 80 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY SIMULATED ANNEALING (80 STRUCTURES) STEP (3) SIMULATED ANNEALING AND ...Details: REFINEMENT PROCEDURE STEP (1) SUBSTRUCTURE EMBEDDING ON 80 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY SIMULATED ANNEALING (80 STRUCTURES) STEP (3) SIMULATED ANNEALING AND ENERGY MINIMIZATION (80 STRUCTURES) STEP (4) RELAXATION MATRIX REFINEMENT ON THE BEST 7 OF 80 STRUCTURES
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 7

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