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- PDB-2ld8: Structure of Human Telomeric DNA in Crowded Solution -

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Basic information

Entry
Database: PDB / ID: 2ld8
TitleStructure of Human Telomeric DNA in Crowded Solution
ComponentsHuman Telomeric DNA
KeywordsDNA / G-quadruplex / propeller-type parallel-stranded / Molecular crowding
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsHeddi, B. / Phan, A.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structure of Human Telomeric DNA in Crowded Solution
Authors: Heddi, B. / Phan, A.T.
History
DepositionMay 17, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 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 1.3May 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

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Human Telomeric DNA


Theoretical massNumber of molelcules
Total (without water)7,2881
Polymers7,2881
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 Human Telomeric DNA


Mass: 7287.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized

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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 NOESY
1312D 1H-1H TOCSY
1412D 1H-1H COSY

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Sample preparation

DetailsContents: 0.2-1mM Human Telomeric DNA, PEG 200/water / Solvent system: PEG 200/water
SampleUnits: mM / Component: Human Telomeric DNA / Conc. range: 0.2-1
Sample conditionspH: 7.00 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AMXBrukerAMX7002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorestructure solution
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
X-PLOR NIHrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 313 / NOE intraresidue total count: 141 / NOE long range total count: 0 / NOE medium range total count: 68 / NOE sequential total count: 104
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.26 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.25 Å / Distance rms dev error: 0.01 Å

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