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- PDB-2kzd: Structure of a (3+1) G-quadruplex formed by hTERT promoter sequence -

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Basic information

Entry
Database: PDB / ID: 2kzd
TitleStructure of a (3+1) G-quadruplex formed by hTERT promoter sequence
ComponentsDNA (5'-D(*AP*GP*GP*GP*IP*AP*GP*GP*GP*GP*CP*TP*GP*GP*GP*AP*GP*GP*GP*C)-3')
KeywordsDNA / anticancer targets / G-quadruplex / hTERT promoter / telomerase inhibition
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, distance-restrained molecular dynamics
Model detailslowest energy, model 1
AuthorsLim, K.W. / Lacroix, L. / Yue, D.J.E. / Lim, J.K.C. / Lim, J.M.W. / Phan, A.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Coexistence of two distinct G-quadruplex conformations in the hTERT promoter
Authors: Lim, K.W. / Lacroix, L. / Yue, D.J.E. / Lim, J.K.C. / Lim, J.M.W. / Phan, A.T.
History
DepositionJun 16, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*GP*GP*IP*AP*GP*GP*GP*GP*CP*TP*GP*GP*GP*AP*GP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,3711
Polymers6,3711
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*AP*GP*GP*GP*IP*AP*GP*GP*GP*GP*CP*TP*GP*GP*GP*AP*GP*GP*GP*C)-3')


Mass: 6371.087 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
1122D 1H-1H NOESY
1212D 1H-1H JR NOESY
1322D 1H-1H COSY
1422D 1H-1H TOCSY
1522D 1H-13C HSQC
1612D 1H-13C JR HMBC
172H-D EXCHANGE
18315N-FILTERED
194D-LABELED

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-2.0 mM DNA-1, 90% H2O/10% D2O90% H2O/10% D2O
20.5-2.0 mM DNA-2, 100% D2O100% D2O
30.5-2.0 mM [U-2% 15N] DNA-3, 90% H2O/10% D2O90% H2O/10% D2O
40.5-2.0 mM [U-100% 2H] DNA-4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDNA-10.5-2.01
mMDNA-20.5-2.02
mMDNA-3[U-2% 15N]0.5-2.03
mMDNA-4[U-100% 2H]0.5-2.04
Sample conditionsIonic strength: 90mM K+ / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospinprocessing
Felix2007Felix NMR, Inc.peak picking
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing, distance-restrained molecular dynamics
Software ordinal: 1
NMR constraintsNA chi-angle constraints total count: 12 / NA epsilon-angle constraints total count: 8 / NA other-angle constraints total count: 12 / NOE constraints total: 508 / Hydrogen bond constraints total count: 52
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.194 Å / Maximum upper distance constraint violation: 0.15 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.014 Å / Distance rms dev error: 0 Å

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