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- PDB-2k71: Structure and dynamics of a DNA GNRA hairpin solved vy high-sensi... -

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Entry
Database: PDB / ID: 2k71
TitleStructure and dynamics of a DNA GNRA hairpin solved vy high-sensitivity NMR with two independent converging methods, simulated annealing (DYANA) and mesoscopic molecular modelling (BCE/AMBER)
Components5'-D(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3'
KeywordsDNA / tetraloop hairpin / B-DNA-like / 2 non canonical torsions / unusual BIIz+ torsions
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, Biopolymer Chain Elasticity approach
Model detailsDNA GNRA tetraloop structure
AuthorsSantini, G.P.H. / Cognet, J.A.H. / Xu, D. / Singarapu, K.K. / Herve du Penhoat, C.L.M.
CitationJournal: J.Phys.Chem.B / Year: 2009
Title: Nucleic acid folding determined by mesoscale modeling and NMR spectroscopy: solution structure of d(GCGAAAGC).
Authors: Santini, G.P. / Cognet, J.A. / Xu, D. / Singarapu, K.K. / Herve du Penhoat, C.
History
DepositionJul 29, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 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'-D(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3'


Theoretical massNumber of molelcules
Total (without water)2,4611
Polymers2,4611
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)21 / 101structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: DNA chain 5'-D(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3'


Mass: 2460.644 Da / Num. of mol.: 1 / Fragment: DNA GNRA hairpin / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: DNA GNRA tetraloop structure
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-13C HSQC
1312D 1H-31P COSY
1412D 1H-1H NOESY
2522D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
14 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride, 100% D2O100% D2O
24 mM dGCGAAAGC, 10 mM sodium phosphate, 0.0025 mM sodium azide, 0.005 mM EDTA, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
4 mMdGCGAAAGC1
10 mMsodium phosphate1
0.0025 mMsodium azide1
0.005 mMEDTA1
50 mMsodium chloride1
4 mMdGCGAAAGC2
10 mMsodium phosphate2
0.0025 mMsodium azide2
0.005 mMEDTA2
50 mMsodium chloride2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 6.8 ambient 298 K
250 6.8 ambient 274 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian UnityVarianUNITY4002

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
PROSAGuntertdata analysis
DYANAGuntert, Braun and Wuthrichrefinement
DYANAGuntert, Braun and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichvisualisation
RefinementMethod: simulated annealing, Biopolymer Chain Elasticity approach
Software ordinal: 1
Details: 100 structures were used in DYANA simulated annealing approach to give models 1 to 20 that were energy-refined with AMBER, Model number 21 was constructed with the BCE approach in agreement ...Details: 100 structures were used in DYANA simulated annealing approach to give models 1 to 20 that were energy-refined with AMBER, Model number 21 was constructed with the BCE approach in agreement with the NMR data and then energy-refined with AMBER
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 101 / Conformers submitted total number: 21

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