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- PDB-5tgg: Solution structure of parallel stranded adenosine duplex -

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Basic information

Entry
Database: PDB / ID: 5tgg
TitleSolution structure of parallel stranded adenosine duplex
ComponentsRNA/DNA (5'-D(P*T)-R(*(A2M)P*(A2M)P*(A2M)P*(A2M))-D(P*A)-R(P*(A2M)P*(A2M)P*(A2M))-3')
KeywordsRNA / DNA / parallel stranded duplex
Function / homologyDNA/RNA hybrid
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsDenisov, A. / Noronha, A. / Gehring, K. / Wilds, C.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.
Authors: Copp, W. / Denisov, A.Y. / Xie, J. / Noronha, A.M. / Liczner, C. / Safaee, N. / Wilds, C.J. / Gehring, K.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Aug 30, 2017Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.7May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA/DNA (5'-D(P*T)-R(*(A2M)P*(A2M)P*(A2M)P*(A2M))-D(P*A)-R(P*(A2M)P*(A2M)P*(A2M))-3')
B: RNA/DNA (5'-D(P*T)-R(*(A2M)P*(A2M)P*(A2M)P*(A2M))-D(P*A)-R(P*(A2M)P*(A2M)P*(A2M))-3')


Theoretical massNumber of molelcules
Total (without water)5,9502
Polymers5,9502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6260 Å2
ΔGint39 kcal/mol
Surface area1370 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 40structures with the least restraint violations and the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: DNA/RNA hybrid RNA/DNA (5'-D(P*T)-R(*(A2M)P*(A2M)P*(A2M)P*(A2M))-D(P*A)-R(P*(A2M)P*(A2M)P*(A2M))-3')


Mass: 2975.072 Da / Num. of mol.: 2 / 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
122isotropic12D DQF-COSY
132isotropic12D 1H-1H TOCSY
142isotropic12D 1H-1H NOESY
252isotropic22D 31P-1H HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM TA8 duplex, 90% H2O/10% D2OTA8_H2O90% H2O/10% D2O
solution21.0 mM TA8 duplex, 100% D2OTA8_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMTA8 duplexnatural abundance1
1.0 mMTA8 duplexnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMconditions_14.0 1 atm283 K
250 mMconditions_24.0 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY8001
Varian VNMRSVarianVNMRS5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations and the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 11

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