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- PDB-1fc8: NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GG... -

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Basic information

Entry
Database: PDB / ID: 1fc8
TitleNMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC)
Components5'-R(*GP*GP*AP*CP)D(*TP*TP*CP*GP*(GFL)P*(TAF)P*(CFL)P*(CFL))-3'
KeywordsRNA/DNA CHIMERA / 2'F-ARABINONUCLEIC ACID / RNA / DNA / HYBRID DUPLEX / HAIRPIN / RNA-DNA CHIMERA COMPLEX
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
MethodSOLUTION NMR / Distance geometry, simulated annealing
AuthorsTrempe, J.-F. / Gehring, K.
CitationJournal: J.Am.Chem.Soc. / Year: 2001
Title: NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes.
Authors: Trempe, J.F. / Wilds, C.J. / Denisov, A.Y. / Pon, R.T. / Damha, M.J. / Gehring, K.
History
DepositionJul 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 5'-R(*GP*GP*AP*CP)D(*TP*TP*CP*GP*(GFL)P*(TAF)P*(CFL)P*(CFL))-3'


Theoretical massNumber of molelcules
Total (without water)3,7901
Polymers3,7901
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)5 / 5RMSD FROM AVERAGE LOWER THAN 0.7 ANGSTROM
RepresentativeModel #3closest to the average

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Components

#1: DNA/RNA hybrid 5'-R(*GP*GP*AP*CP)D(*TP*TP*CP*GP*(GFL)P*(TAF)P*(CFL)P*(CFL))-3' / RNA/2'F-ANA HAIRPIN


Mass: 3790.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SOLID PHASE SYNTHESIS; PHOSPHORAMIDITE CHEMISTRY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
132DQF-COSY
1422D 1H-13C HMQC
1522D 1H-31P HETCOR
1622D 1H-19F HETCOR
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM Oligonucleotide hairpin; 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM Oligonucleotide hairpin; D2OD2O
Sample conditionsIonic strength: 0.066 / pH: 7.2 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX4002
Varian UNITYPLUSVarianUNITYPLUS7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.843BRUNGERstructure solution
X-PLOR3.843BRUNGERrefinement
RefinementMethod: Distance geometry, simulated annealing / Software ordinal: 1
Details: SA at 15000K for 15 psec from random coordinates. Refinement from lower energy structure at 3000K fro 9 psec. 5 structures generated. Total of 305 restraints: 98 intraresidue NOE-derived ...Details: SA at 15000K for 15 psec from random coordinates. Refinement from lower energy structure at 3000K fro 9 psec. 5 structures generated. Total of 305 restraints: 98 intraresidue NOE-derived distance constraints, 94 sequential NOE-derived distance constraints, 3 long range NOE-derived distance constraints, 15 distance restraints from hydrogen bonds, 91 dihedral angle restraints, 4 planarity constraints for base pairs
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: RMSD FROM AVERAGE LOWER THAN 0.7 ANGSTROM
Conformers calculated total number: 5 / Conformers submitted total number: 5

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