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- PDB-1aff: DNA QUADRUPLEX CONTAINING GGGG TETRADS AND (T.A).A TRIADS, NMR, 8... -

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Basic information

Entry
Database: PDB / ID: 1aff
TitleDNA QUADRUPLEX CONTAINING GGGG TETRADS AND (T.A).A TRIADS, NMR, 8 STRUCTURES
ComponentsQUADRUPLEX DNA (5'-D(TP*AP*GP*G)-3')
KeywordsDNA / DNA-QUADRUPLEX / (T.A).A BASE TRIAD / BOMBYX MORI TELOMERIQUE SINGLE REPEAT / T-A PLATFORM / DEOXYRIBONUCLEIC ACID
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT, RELAXATION MATRIX INTENSITY REFINEMENT
AuthorsKettani, A. / Bouaziz, S. / Wang, W. / Jones, R.A. / Patel, D.J.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads.
Authors: Kettani, A. / Bouaziz, S. / Wang, W. / Jones, R.A. / Patel, D.J.
History
DepositionMar 6, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: 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: QUADRUPLEX DNA (5'-D(TP*AP*GP*G)-3')
B: QUADRUPLEX DNA (5'-D(TP*AP*GP*G)-3')
C: QUADRUPLEX DNA (5'-D(TP*AP*GP*G)-3')
D: QUADRUPLEX DNA (5'-D(TP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,9234
Polymers4,9234
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 / 100LEAST ENERGY AND LEAST RESTRAINT VIOLATIONS
Representative

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Components

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


Mass: 1230.854 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: TRUNCATED BIOLOGICAL SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
1411H-31P COSY
NMR detailsText: STRUCTURE DETERMINED USING NMR EXPERIMENTS IN D2O: NOESY, COSY, TOCSY AND 1H-31P COSY. NOESY BUILDUP AT 50, 100, 150, 200 AND 300 MS. NMR EXPERIMENTS IN H2O: NOESY (60, 120 AND 200 MS)

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Sample preparation

Sample conditionspH: 6.2 / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / 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, SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT, RELAXATION MATRIX INTENSITY REFINEMENT
Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST ENERGY AND LEAST RESTRAINT VIOLATIONS
Conformers calculated total number: 100 / Conformers submitted total number: 8

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