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- PDB-6rs3: 2'-F-riboguanosine modified G-quadruplex with V-loop -

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Basic information

Entry
Database: PDB / ID: 6rs3
Title2'-F-riboguanosine modified G-quadruplex with V-loop
ComponentsF1415
KeywordsDNA / G-quadruplex / V-loop
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsHaase, L. / Weisz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationDFG WE 1933/15-1 Germany
CitationJournal: Chemistry / Year: 2020
Title: Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops.
Authors: Haase, L. / Dickerhoff, J. / Weisz, K.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F1415


Theoretical massNumber of molelcules
Total (without water)7,0081
Polymers7,0081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: no quaternary structure
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3780 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain F1415


Mass: 7008.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC aromatic
241isotropic12D 1H-13C HSQC aromatic
152isotropic12D DQF-COSY
161isotropic12D 1H-13C HMBC
271isotropic12D 1H-13C HMBC
182isotropic12D 1H-1H NOESY
293isotropic11D 1H-15N HMBC
2104isotropic11D 1H-15N HMBC
2115isotropic11D 1H-15N HMBC
2126isotropic11D 1H-15N HMBC
2137isotropic11D 1H-15N HMBC
2148isotropic11D 1H-15N HMBC
2159isotropic11D 1H-15N HMBC
21610isotropic11D 1H-15N HMBC
21711isotropic11D 1H-15N HMBC
21812isotropic11D 1H-15N HMBC
21913isotropic11D 1H-15N HMBC
12013isotropic11D 1H-15N HMBC
22114isotropic11D 1H-15N HMBC
12214isotropic11D 1H-15N HMBC
22315isotropic11D 1H-15N HMBC
12415isotropic11D 1H-15N HMBC
22516isotropic12D 1H-13C HSQC aromatic
12616isotropic12D 1H-13C HSQC aromatic
22717isotropic12D 1H-13C HSQC aromatic
12817isotropic12D 1H-13C HSQC aromatic
22916isotropic12D DQF-COSY
13016isotropic12D DQF-COSY
23117isotropic12D DQF-COSY
13217isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM F1415, 90% H2O/10% D2OF141590% H2O/10% D2O
solution21.0 mM F1415, 100% D2OF1415_ex100% D2O
solution30.2 mM 15N 10% G1 F1415, 90% H2O/10% D2OF1415(1)90% H2O/10% D2O
solution40.2 mM 15N 10% G2 F1415, 90% H2O/10% D2OF1415(2)90% H2O/10% D2O
solution50.2 mM 15N 10% G3 F1415, 90% H2O/10% D2OF1415(3)90% H2O/10% D2O
solution60.2 mM 15N 10% G6 F1415, 90% H2O/10% D2OF1415(6)90% H2O/10% D2O
solution70.2 mM 15N 10% G17 F1415, 90% H2O/10% D2OF1415(7)90% H2O/10% D2O
solution80.2 mM 15N 10% G8 F1415, 90% H2O/10% D2OF1415(8)90% H2O/10% D2O
solution90.2 mM 15N 10% G16 F1415, 90% H2O/10% D2OF1415(16)90% H2O/10% D2O
solution100.2 mM 15N 10% G17 F1415, 90% H2O/10% D2OF1415(17)90% H2O/10% D2O
solution110.2 mM 15N 10% G20 F1415, 90% H2O/10% D2OF1415(20)90% H2O/10% D2O
solution120.2 mM 15N 10% G21 F1415, 90% H2O/10% D2OF1415(21)90% H2O/10% D2O
solution130.2 mM 15N 10% A9 F1415, 90% H2O/10% D2OF1415(A9)90% H2O/10% D2O
solution140.2 mM 15N 10% A11 F1415, 90% H2O/10% D2OF1415(A11)90% H2O/10% D2O
solution150.2 mM 15N 10% A13 F1415, 90% H2O/10% D2OF1415(A13)90% H2O/10% D2O
solution160.4 mM F1415(10MeC), 90% H2O/10% D2OF1415(10MeC)90% H2O/10% D2O
solution170.4 mM F1415(12MeC), 90% H2O/10% D2OF1415(12MeC)90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMF1415natural abundance1
1.0 mMF1415natural abundance2
0.2 mMF141515N 10% G13
0.2 mMF141515N 10% G24
0.2 mMF141515N 10% G35
0.2 mMF141515N 10% G66
0.2 mMF141515N 10% G177
0.2 mMF141515N 10% G88
0.2 mMF141515N 10% G169
0.2 mMF141515N 10% G1710
0.2 mMF141515N 10% G2011
0.2 mMF141515N 10% G2112
0.2 mMF141515N 10% A913
0.2 mMF141515N 10% A1114
0.2 mMF141515N 10% A1315
0.4 mMF1415(10MeC)natural abundance16
0.4 mMF1415(12MeC)natural abundance17
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mM potassium phosphate buffer at pH 715 mM40deg10mMKP71 atm313 K
210 mM potassium phosphate buffer at pH 715 mM25deg10mMKP71 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: Cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.0.4Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNchemical shift assignment
Xplor-NIH2.49Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing3
molecular dynamics4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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