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- PDB-2mfu: Solution NMR structure of quadruplex d(TGGGTTTGGGTTGGGTTTGGG) in ... -

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Basic information

Entry
Database: PDB / ID: 2mfu
TitleSolution NMR structure of quadruplex d(TGGGTTTGGGTTGGGTTTGGG) in sodium conditions
Components5'-D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3'
KeywordsDNA / G-Quadruplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsKarsisiotis, A. / Dillon, P. / Webba da Silva, M.
CitationJournal: To be Published
Title: Solution NMR structure of quadruplex d(TGGGTTTGGGTTGGGTTTGGG) in sodium conditions
Authors: Karsisiotis, A. / Dillon, P. / Webba da Silva, M.
History
DepositionOct 23, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,6431
Polymers6,6431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 6643.248 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
2122D 1H-1H TOCSY
2222D 1H-1H DQF-COSY
2322D 1H-1H NOESY
1412D 1H-1H NOESY
2522D 1H-31P HSQC
1612D 1H-13C HMBC (H1-H8 long range correlation)

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Sample preparation

Details
Solution-IDContentsSolvent system
15-6 mM D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3', 20 mM sodium phosphate, 70 mM sodium chloride, 93% H2O/7% D2O93% H2O/7% D2O
25-6 mM D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3', 20 mM sodium phosphate, 70 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mM5'-D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3'-15-61
20 mMsodium phosphate-21
70 mMsodium chloride-31
mM5'-D(*TP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3'-45-62
20 mMsodium phosphate-52
70 mMsodium chloride-62
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
195 6.8 ambient 278 K
295 6.8 ambient 293 K

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NMR measurement

NMR spectrometerType: Varian VNMRS 500 / Manufacturer: Varian / Model: VNMRS 500 / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.data analysis
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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