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- PDB-5zld: SOLUTION NMR STRUCTURE OF A 14-MER DOUBLE STRANDED DNA DUPLEX CGC... -

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Basic information

Entry
Database: PDB / ID: 5zld
TitleSOLUTION NMR STRUCTURE OF A 14-MER DOUBLE STRANDED DNA DUPLEX CGCGAAATTTCGCG
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGanguly, S. / Basu, G.
CitationJournal: Biochemistry / Year: 2021
Title: DNA Minor Groove-Induced cis - trans Isomerization of a Near-Infrared Fluorescent Probe.
Authors: Ganguly, S. / Murugan, N.A. / Ghosh, D. / Narayanaswamy, N. / Govindaraju, T. / Basu, G.
History
DepositionMar 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)8,5622
Polymers8,5622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: The double stranded structure of the DNA was confirmed from the presence of sharp imino peaks in NMR spectra
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1310 Å2
ΔGint-9 kcal/mol
Surface area5420 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4280.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
221isotropic12D 1H-1H TOCSY
242isotropic12D 1H-1H NOESY
252isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1300 uM 1H DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3'), 90% H2O/10% D2ODNA oligonucleotide was annealed in buffer containing 10mM sodium phosphate and 10mM sodium chloride (pH 7.0).1H_sample90% H2O/10% D2O
solution2300 uM 1H DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3'), 100% D2OdsDNA annealed in buffer (10mM sodium phosphate, 10mM sodium chloride, pH 7) was lyophilised and redissolved in 100% deuterium oxide.1H_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMDNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3')1H1
300 uMDNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*CP*GP*CP*G)-3')1H2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mM NaCl mMconditions_17.0 1 atm298 K
210mM NaCl mMconditions_27.0 pD1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz
Details: Avance III HD NMR spectrophotometer equipped with cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospindata analysis
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 4

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