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- PDB-2ms9: Solution structure of a G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 2ms9
TitleSolution structure of a G-quadruplex
ComponentsDNA (28-MER)
KeywordsDNA / G-quadruplex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic (others)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, Distance-restrained molecular dynamics
Model detailslowest energy, model1
AuthorsChung, W.J. / Heddi, B. / Schmitt, E. / Lim, K.W. / Mechulam, Y. / Phan, A.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of a left-handed DNA G-quadruplex
Authors: Chung, W.J. / Heddi, B. / Schmitt, E. / Lim, K.W. / Mechulam, Y. / Phan, A.T.
History
DepositionJul 25, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)8,8731
Polymers8,8731
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (28-MER)


Mass: 8872.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H JR NOESY
1222D 1H-1H NOESY
1322D 1H-1H TOCSY
1422D 1H-13C HSQC aliphatic
1522D 1H-13C HSQC aromatic
1612D 1H-13C JR HMBC
17115N-FILTERED
181D-LABELED

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3, 90% H2O/10% D2O90% H2O/10% D2O
20.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMDNA (28-MER)-10.2-21
mMDNA (28-MER)-2[U-2% 15N]0.2-0.51
mMDNA (28-MER)-3[U-100% 2H]0.2-0.51
mMDNA (28-MER)-40.2-22
mMDNA (28-MER)-5[U-4% 13C; U-4% 15N]0.2-12
Sample conditionsIonic strength: 90 / pH: 7 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing, Distance-restrained molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 664 / NOE intraresidue total count: 313 / Hydrogen bond constraints total count: 64
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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