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- PDB-1evm: NMR OBSERVATION OF A-TETRAD -

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Basic information

Entry
Database: PDB / ID: 1evm
TitleNMR OBSERVATION OF A-TETRAD
ComponentsDNA (5'-D(*AP*GP*GP*GP*T)-3')
KeywordsDNA / A-tetrad / G-Quadruplex / Human telomere
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / Restrained energy minimizatiom, simulated annealing-restrained molecular dynamics, Iterative relaxation matrix refinement
AuthorsPatel, P.K. / Koti, A.S.R. / Hosur, R.V.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: NMR studies on truncated sequences of human telomeric DNA: observation of a novel A-tetrad.
Authors: Patel, P.K. / Koti, A.S. / Hosur, R.V.
History
DepositionApr 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 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
M: DNA (5'-D(*AP*GP*GP*GP*T)-3')
N: DNA (5'-D(*AP*GP*GP*GP*T)-3')
O: DNA (5'-D(*AP*GP*GP*GP*T)-3')
P: DNA (5'-D(*AP*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)6,2404
Polymers6,2404
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 / 8structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: DNA chain
DNA (5'-D(*AP*GP*GP*GP*T)-3')


Mass: 1560.060 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: PARALLEL STRANDED DNA QUADRUPLEX STRUCTURE INCORPORATING A-TETRAD

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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
242E-COSY
NMR detailsText: temperature dependance 1D, pH dependance 1D and salt dependance 1D. Temperature varied from 0 to 70 C

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM potassium phosphate, 0.2 mM EDTA, 2-100 mM KCl, pH 7.390% H2O and 10% D2O
22mM potassium phosphate, 0.2 mM EDTA, 2-100 mM KCl, pH 7.3D2O
Sample conditionspH: 7.3 / Pressure: 1 atm / Temperature units: 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
VNMR6.1Variancollection
Felix230 and 97BIOSYMdata analysis
XwinNMR1.3Brukercollection
Discover3.1BIOSYMstructure solution
IRMA2.3BIOSYMiterative matrix relaxation
Discover3.1BIOSYMrefinement
RefinementMethod: Restrained energy minimizatiom, simulated annealing-restrained molecular dynamics, Iterative relaxation matrix refinement
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 8 / Conformers submitted total number: 8

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