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- PDB-1oz8: Intramolecular higher-order packing of parallel quadruplexes comp... -

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Basic information

Entry
Database: PDB / ID: 1oz8
TitleIntramolecular higher-order packing of parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad of GGA triplet repeat DNA
Components5'-D(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3'
KeywordsDNA / intramolecular packing of parallel quadruplexes
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsMatsugami, A. / Okuizumi, T. / Uesugi, S. / Katahira, M.
Citation
Journal: J.BIOL.CHEM. / Year: 2003
Title: Intramolecular Higher Order Packing of Parallel Quadruplexes Comprising a G:G:G:G Tetrad and a G(:A):G(:A):G(:A):G Heptad of GGA Triplet Repeat DNA
Authors: Matsugami, A. / Okuizumi, T. / Uesugi, S. / Katahira, M.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: An Intramolecular Quadruplex of (GGA)(4) Triplet Repeat DNA with a G:G:G:G Tetrad and a G(:A):G(:A):G(:A):G Heptad, and its Dimeric Interaction
Authors: Matsugami, A. / Ouhashi, K. / Kanagawa, M. / Liu, H. / Kanagawa, S. / Uesugi, S. / Katahira, M.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: A Dimeric RNA Quadruplex Architecture Comprised of Two G:G(:A):G:G(:A) Hexads, G:G:G:G Tetrads and UUUU Loops
Authors: Liu, H. / Matsugami, A. / Katahira, M. / Uesugi, S.
History
DepositionApr 8, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 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: 5'-D(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3'


Theoretical massNumber of molelcules
Total (without water)7,7281
Polymers7,7281
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3'


Mass: 7727.991 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
2322D TOCSY
242DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM DNA; 10mM sodium phosphate buffer; 30mM KCl95% H2O/5% D2O
21mM DNA; 10mM sodium phosphate buffer; 30mM KCl100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5ambient 275 K
26.5ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
X-PLOR3.851refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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