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- PDB-2gku: Monomeric human telomere DNA tetraplex with 3+1 strand fold topol... -

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Entry
Database: PDB / ID: 2gku
TitleMonomeric human telomere DNA tetraplex with 3+1 strand fold topology, two edgewise loops and double-chain reversal loop, NMR, 12 structures
ComponentsHuman telomere DNA
KeywordsDNA / G-TETRAD / 3+1 STRAND FOLDING / EDGEWISE / DOUBLE-CHAIN REVERSAL LOOPS / NMR / 12 STRUCTURES
Specimen sourceHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS CARTESIAN DYNAMICS MATRIX RELAXATION
AuthorsLuu, K.N. / Phan, A.T. / Kuryavyi, V.V. / Lacroix, L. / Patel, D.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Structure of the human telomere in k(+) solution: an intramolecular (3 + 1) g-quadruplex scaffold.
Authors: Luu, K.N. / Phan, A.T. / Kuryavyi, V.V. / Lacroix, L. / Patel, D.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 3, 2006 / Release: Aug 15, 2006
RevisionDateData content typeGroupProviderType
1.0Aug 15, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: Human telomere DNA


Theoretical massNumber of molelcules
Total (without water)7,5921
Polyers7,5921
Non-polymers00
Water0
NMR ensembles
Datacriteria
Number of conformers (submitted / calculated)12 / 50back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

#1: DNA chain Human telomere DNA


Mass: 7591.883 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1

Experiment-IDSolution-IDType
111H-1H NOESY
221H-1H TOCSY
321H-31P COSY
421H-1H COSY
511H-15N JRHMQC
621H-15N HMBC

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Sample preparation

Details
Solution-IDContentsSolvent system
170 MM KCL 20 MM POTASSIUM PHOSPHATE 90% H2O 10% D2O90% H2O/10% D2O
270 MM KCL 20 MM POTASSIUM PHOSPHATE 100% D2O100% D2O
sample conditionsIonic strength: 70 mM / pH: 7.0 / Pressure: 1 atm / Temperature: 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
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAvance8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6VARIANcollection
FELIX2000ACCELRYSdata analysis
X-PLOR3.851AT BRUNGERstructure solution
X-PLOR3.851AT BRUNGERrefinement
RefinementMethod: TORSION ANGLE DYNAMICS CARTESIAN DYNAMICS MATRIX RELAXATION
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 50 / Conformers submitted total number: 12

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