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- PDB-6ffr: DNA-RNA Hybrid Quadruplex with Flipped Tetrad -

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Basic information

Entry
Database: PDB / ID: 6ffr
TitleDNA-RNA Hybrid Quadruplex with Flipped Tetrad
ComponentsDNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')
KeywordsDNA-RNA HYBRID / quadruplex
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing / simulated annealing
AuthorsHaase, L. / Dickerhoff, J. / Weisz, K.
CitationJournal: Chemistry / Year: 2018
Title: DNA-RNA Hybrid Quadruplexes Reveal Interactions that Favor RNA Parallel Topologies.
Authors: Haase, L. / Dickerhoff, J. / Weisz, K.
History
DepositionJan 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,0041
Polymers7,0041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3720 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')


Mass: 7004.491 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 mixing time 500 ms
121isotropic12D 1H-1H NOESY mixing time 300 ms
131isotropic12D 1H-1H NOESY mixing time 150 ms
141isotropic12D 1H-1H NOESY mixing time 80 ms
151isotropic12D 1H-13C HSQC aromatic
162isotropic12D 1H-1H NOESY mixing time 300 ms
172isotropic12D 1H-13C HSQC aromatic
182isotropic12D DQF-COSY
192isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3'), 90% H2O/10% D2Oodn_r_1_2090% H2O/10% D2O
solution210 mM potassium phosphate, 0.48 mM DNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3'), 100% D2Oodn_r_1_20_ex100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMpotassium phosphatenatural abundance1
0.48 mMDNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')natural abundance1
10 mMpotassium phosphatenatural abundance2
0.48 mMDNA/RNA (5'-R(*G)-D(P*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*C)-R(P*G)-D(P*GP*G)-3')natural abundance2
Sample conditionsIonic strength: 10 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospinprocessing
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr Analysis2.4CCPNpeak picking
Xplor-NIH2.46Schwieters, Kuszewski, Tjandra and Clorerefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Refinement
MethodSoftware ordinal
DGSA-distance geometry simulated annealing4
simulated annealing5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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