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- PDB-1a8w: A K+ CATION-INDUCED CONFORMATIONAL SWITCH WITHIN A LOOP SPANNING ... -

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Basic information

Entry
Database: PDB / ID: 1a8w
TitleA K+ CATION-INDUCED CONFORMATIONAL SWITCH WITHIN A LOOP SPANNING SEGMENT OF A DNA QUADRUPLEX CONTAINING G-G-G-C REPEATS, NMR, 8 STRUCTURES
ComponentsDNA QUADRUPLEX CONTAINING GGGG TETRADS AND GC WATSON-CRICK BASE PAIRS
KeywordsDNA / CATION DEPENDENT CONFORMATIONAL TRANSITIONS / K+ CATION COORDINATION SITES / K+ CATION ENCAPSULATION WITHIN A HAIRPIN LOOP / DNA QUADRUPLEXES TARGETED TO HIV INTEGRASE / DEOXYRIBONUCLEIC ACID / G-G-G-C REPEAT-CONTAINING DNA QUADRUPLEXES / MONOVALENT
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry
AuthorsBouaziz, S. / Kettani, A. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats.
Authors: Bouaziz, S. / Kettani, A. / Patel, D.J.
History
DepositionMar 28, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: 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: DNA QUADRUPLEX CONTAINING GGGG TETRADS AND GC WATSON-CRICK BASE PAIRS
B: DNA QUADRUPLEX CONTAINING GGGG TETRADS AND GC WATSON-CRICK BASE PAIRS


Theoretical massNumber of molelcules
Total (without water)7,4512
Polymers7,4512
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 / 100ACCEPTABLE COVALENT ENERGY, LOW DISTANCE RESTRAINT VIOLATIONS, FAVORABLE NON-BONDED ENERGY
Representative

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Components

#1: DNA chain DNA QUADRUPLEX CONTAINING GGGG TETRADS AND GC WATSON-CRICK BASE PAIRS


Mass: 3725.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: K+ CATION STABILIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
NMR detailsText: STRUCTURE DETERMINED BY USING 5 NOESY MIXING TIME EXPERIMENTS IN D2O (50, 100, 150, 200 AND 300 MS) AND 2 NOESY MIXING TIME EXPERIMENTS IN H2O (80 AND 250 MS)

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Sample preparation

DetailsContents: 5 MM NACL, 0.2 MM NA2HPO4
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY INOVA / Manufacturer: Varian / Model: UNITY INOVA / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: ACCEPTABLE COVALENT ENERGY, LOW DISTANCE RESTRAINT VIOLATIONS, FAVORABLE NON-BONDED ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 8

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