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- PDB-2m53: G-rich VEGF aptamer with LNA modifications -

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Basic information

Entry
Database: PDB / ID: 2m53
TitleG-rich VEGF aptamer with LNA modifications
ComponentsG-rich VEGF aptamer
KeywordsDNA / aptamer / G-quadruplex / locked nucleic acid / VEGF
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsMarusic, M. / Veedu, R.N. / Plavec, J.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: G-rich VEGF aptamer with locked and unlocked nucleic acid modifications exhibits a unique G-quadruplex fold.
Authors: Marusic, M. / Veedu, R.N. / Wengel, J. / Plavec, J.
History
DepositionFeb 13, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_nmr_software ...pdbx_entity_src_syn / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer ..._pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-rich VEGF aptamer


Theoretical massNumber of molelcules
Total (without water)8,0011
Polymers8,0011
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 least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: DNA chain G-rich VEGF aptamer


Mass: 8001.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2132D 1H-1H NOESY
2232D DQF-COSY
2332D 1H-1H TOCSY
2412D 1H-1H NOESY
3522D 1H-1H NOESY
1612D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM DNA(25-MER)-1, 10 mM potassium phosphate-2, 90 mM potassium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM DNA(25-MER)-4, 10 mM potassium phosphate-5, 40 mM potassium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM DNA(25-MER)-7, 10 mM potassium phosphate-8, 90 mM potassium chloride-9, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMDNA(25-MER)-11
10 mMpotassium phosphate-21
90 mMpotassium chloride-31
0.5 mMDNA(25-MER)-42
10 mMpotassium phosphate-52
40 mMpotassium chloride-62
0.5 mMDNA(25-MER)-73
10 mMpotassium phosphate-83
90 mMpotassium chloride-93
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11007ambient 273 K
21007ambient 298 K
3507ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS6001
Varian VNMRSVarianVNMRS8002

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Processing

NMR software
NameVersionDeveloperClassification
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmandata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
VnmrJAgilent Technologiescollection
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: 25 / NA delta-angle constraints total count: 0 / NA epsilon-angle constraints total count: 24 / NA gamma-angle constraints total count: 0 / NA other-angle constraints total count: 0 / NA sugar pucker constraints total count: 12 / NOE constraints total: 250 / NOE intraresidue total count: 143 / NOE long range total count: 27 / NOE medium range total count: 24 / NOE sequential total count: 54 / Hydrogen bond constraints total count: 0
NMR representativeSelection criteria: fewest violations
NMR ensembleAverage torsion angle constraint violation: 2.804 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.176 Å / Maximum torsion angle constraint violation: 4.274 ° / Maximum upper distance constraint violation: 0.109 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.083 Å / Distance rms dev error: 0.029 Å

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