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- PDB-1f5h: The G7(syn)-G4(anti) structure of r(GCAGGCGUGC)2 -

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Entry
Database: PDB / ID: 1f5h
TitleThe G7(syn)-G4(anti) structure of r(GCAGGCGUGC)2
Components5'-R(*GP*CP*AP*GP*GP*CP*GP*UP*GP*C)-3'
KeywordsRNA / GUANINE-GUANINE / GG MISMATCH / CONFORMATIONAL EXCHANGE / BASE FLIPPING / syn GLYCOSIDIC TORSION
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / Simulated annealing; Energy minimization
Model type detailsminimized average
AuthorsBurkard, M.E. / Turner, D.H.
Citation
Journal: Biochemistry / Year: 2000
Title: NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs
Authors: Burkard, M.E. / Turner, D.H.
#1: Journal: Biochemistry / Year: 1999
Title: Thermodyamics of single mismatches in RNA duplexes
Authors: Kierzek, R. / Burkard, M.E. / Turner, D.H.
History
DepositionJun 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 16, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*CP*AP*GP*GP*CP*GP*UP*GP*C)-3'
B: 5'-R(*GP*CP*AP*GP*GP*CP*GP*UP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,4642
Polymers6,4642
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)26 / 40structures with the lowest energy. First model represents the minimized averaged structure
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain 5'-R(*GP*CP*AP*GP*GP*CP*GP*UP*GP*C)-3'


Mass: 3231.988 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 NOESY
121DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 80 mM NaCl; 10 mM phosphate, pH 7 / Solvent system: D2O
Sample conditionsIonic strength: 80 mM / pH: 7 / Pressure: ambient / Temperature: 310.15 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.2Variancollection
Felix95Biosymdata analysis
Discover95Biosymstructure solution
Discover95Biosymrefinement
RefinementMethod: Simulated annealing; Energy minimization / Software ordinal: 1
Details: The structures are based on 88 NOE distance restraints, 11 hydrogen-bond restraints for Watson-Crick pairs, and loosely restrained torsion angles. 22 of 25 structures were used to generate ...Details: The structures are based on 88 NOE distance restraints, 11 hydrogen-bond restraints for Watson-Crick pairs, and loosely restrained torsion angles. 22 of 25 structures were used to generate the minimized, averaged structure. G4 was restrained to the syn glycosidic conformation
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy. First model represents the minimized averaged structure
Conformers calculated total number: 40 / Conformers submitted total number: 26

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