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- PDB-2lod: Solution-state structure of an intramolecular G-quadruplex with p... -

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Basic information

Entry
Database: PDB / ID: 2lod
TitleSolution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops
ComponentsDNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*CP*GP*GP*G)-3')
KeywordsDNA / G-QUADRUPLEX / LOOPS
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMarusic, M. / Sket, P. / Bauer, L. / Viglasky, V. / Plavec, J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops.
Authors: Marusic, M. / Sket, P. / Bauer, L. / Viglasky, V. / Plavec, J.
History
DepositionJan 23, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*CP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,9721
Polymers6,9721
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 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*GP*AP*CP*GP*GP*G)-3')


Mass: 6972.491 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
1222D 1H-1H NOESY
1322D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.7 mM DG3ATG3ACACAG4ACG3, 10 mM potassium phosphate, 40 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
22.3 mM DG3ATG3ACACAG4ACG3, 10 mM potassium phosphate, 40 mM potassium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 mMpotassium phosphate-11
40 mMpotassium chloride-21
10 mMpotassium phosphate-32
40 mMpotassium chloride-42
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVarianprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 0 / NA beta-angle constraints total count: 0 / NA chi-angle constraints total count: 22 / NA delta-angle constraints total count: 0 / NA epsilon-angle constraints total count: 21 / NA gamma-angle constraints total count: 0 / NA other-angle constraints total count: 36 / NA sugar pucker constraints total count: 22 / NOE constraints total: 316 / NOE intraresidue total count: 216 / NOE long range total count: 19 / NOE medium range total count: 11 / NOE sequential total count: 70 / Hydrogen bond constraints total count: 24
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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