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- PDB-5gwq: Structure of two TTTA repeats -

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Basic information

Entry
Database: PDB / ID: 5gwq
TitleStructure of two TTTA repeats
ComponentsDNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3')
KeywordsDNA / Minidumbbell / type II loop
Function / homologyDNA
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / restrained molecular dynamics
AuthorsGuo, P. / Lam, S.L.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Research Grants Council of HKSARGRF CUHK14302114 and CUHK14302915 Hong Kong
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Minidumbbell: A New Form of Native DNA Structure
Authors: Guo, P. / Lam, S.L.
History
DepositionSep 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_prerelease_seq / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5688
Polymers2,4071
Non-polymers1617
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area860 Å2
ΔGint-73 kcal/mol
Surface area1480 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3')


Mass: 2406.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic22D DQF-COSY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM DNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3'), 10 mM sodium phosphate, 0.1 mM DSS, 100% D2O
Label: 1H / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMDNA (5'-D(*TP*TP*TP*AP*TP*TP*TP*A)-3')natural abundance1
10 mMsodium phosphatenatural abundance1
0.1 mMDSSnatural abundance1
Sample conditionsIonic strength: 0.02 M / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIBrukerAVANCE II5002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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