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- PDB-1emq: NMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA QUADRUPLE... -

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Basic information

Entry
Database: PDB / ID: 1emq
TitleNMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA QUADRUPLEX FORMED BY SACCHAROMYCES CEREVISIAE TELOMERE REPEATS
ComponentsDNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')
KeywordsDNA / T-tetrad / G-quadruplex / Telomere / Yeast / Saccharomyces cerevisiae
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / An initial model of quadruplex was generated on a IRIS workastation.Energy minimization by steepest descent, conjugate gradients methods was done using AMBER force field. Conformational search for the cquadruplex was performed by simulated annealing-reastarined molecular dynamics using AMBER forcefield. Relaxation matrix refinement was performed.
Model type detailsminimized average
AuthorsHosur, R.V. / Patel, P.K.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: NMR observation of T-tetrads in a parallel stranded DNA quadruplex formed by Saccharomyces cerevisiae telomere repeats.
Authors: Patel, P.K. / Hosur, R.V.
History
DepositionMar 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')
B: DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')
C: DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')
D: DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)8,6784
Polymers8,6784
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)1 / 8structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 2169.433 Da / Num. of mol.: 4 / Fragment: YEAST TELOMERE REPEATS / Source method: obtained synthetically
Details: This sequence is two repeats of Saccharomyces cerevisiae telomere sequence

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121E-COSY
1312D-TOCSY
NMR detailsText: 0-70 C Temperature dependent one dimensional spectra. pH dependent spectra.

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM DNA in 0.6 ml(90%H20/10%D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KCl90% H2O/10% D2O
21-2 mM DNA in 0.6 ml(D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KClD2O
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
Felix230MSIprocessing
VNMR6.1Variancollection
Discover3.1MSIstructure solution
IRMA2.3MSIrefinement
RefinementMethod: An initial model of quadruplex was generated on a IRIS workastation.Energy minimization by steepest descent, conjugate gradients methods was done using AMBER force field. Conformational ...Method: An initial model of quadruplex was generated on a IRIS workastation.Energy minimization by steepest descent, conjugate gradients methods was done using AMBER force field. Conformational search for the cquadruplex was performed by simulated annealing-reastarined molecular dynamics using AMBER forcefield. Relaxation matrix refinement was performed.
Software ordinal: 1
Details: A total of 234 NOEs constarint. 20 hydrogen bonds constraints. 8 convergant structure after IRMA refinement. R1 factor = 0.31-0.33. r.m.s.d.s from average structure 0.2-0.4. Nil violation exceeding 0.2 A.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 8 / Conformers submitted total number: 1

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