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- PDB-2lpw: human CEB25 minisatellite G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 2lpw
Titlehuman CEB25 minisatellite G-quadruplex
ComponentsDNA (26-MER)
KeywordsDNA / G-quadruplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsAmrane, S. / Adrian, M. / Heddi, B. / Serero, A. / Nicolas, A. / Mergny, J.L. / Phan, A.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Formation of Pearl-Necklace Monomorphic G-Quadruplexes in the Human CEB25 Minisatellite.
Authors: Amrane, S. / Adrian, M. / Heddi, B. / Serero, A. / Nicolas, A. / Mergny, J.L. / Phan, A.T.
History
DepositionFeb 20, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)8,2751
Polymers8,2751
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 (26-MER)


Mass: 8275.308 Da / Num. of mol.: 1 / 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 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-13C HSQC
1412D 1H-1H COSY
1512D 1H-13C HSQC
1612D 1H-31P-HSQC
1712D 1H-13C-HMBC

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Sample preparation

DetailsContents: 0.2-2 mM DNA (26-MER), 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: DNA (26-MER)-1 / Conc. range: 0.2-2
Sample conditionsIonic strength: 90 / pH: 7.00 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX4001
Bruker AMXBrukerAMX6002
Bruker AMXBrukerAMX7003
Bruker AMXBrukerAMX8004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Cloredata analysis
SparkyGoddardstructure solution
SparkyGoddarddata analysis
FelixAccelrys Software Inc.structure solution
FelixAccelrys Software Inc.data analysis
FelixSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1 / Details: DGSA-distance geometry simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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