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- PDB-2m1g: Parallel human telomeric quadruplex containing 2'F-ANA substitutions -

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Basic information

Entry
Database: PDB / ID: 2m1g
TitleParallel human telomeric quadruplex containing 2'F-ANA substitutions
Components5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3'
KeywordsDNA / parallel G-quadruplex / human telomeric sequence / fluoro-arabinose / molecular interactions
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailsclosest to the average
AuthorsMartin-Pintado, N. / Yahyaee-Anzahaee, M. / Deleavey, G.F. / Portella, G. / Orozco, M. / Damha, M.J. / Gonzalez, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Dramatic effect of furanose c2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom.
Authors: Martin-Pintado, N. / Yahyaee-Anzahaee, M. / Deleavey, G.F. / Portella, G. / Orozco, M. / Damha, M.J. / Gonzalez, C.
History
DepositionNov 27, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3'
B: 5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,5832
Polymers7,5832
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 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 3791.453 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H TOCSY
1322D DQF-COSY
1422D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3'), 5 mM potassium chloride, 10 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3'), 10 mM potassium chloride, 5 mM potassium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.7 mMDNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3')-11
5 mMpotassium chloride-21
10 mMpotassium phosphate-31
0.7 mMDNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(GFL)P*GP*GP*T)-3')-42
10 mMpotassium chloride-52
5 mMpotassium phosphate-62
Sample conditionsIonic strength: 15 / pH: 7 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
SparkyGoddardchemical shift assignment
MOLMOLKoradi, Billeter and Wuthrichdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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