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- PDB-7ogv: A self-complementary DNA dodecamer duplex contaning 5-hydroxymeth... -

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Basic information

Entry
Database: PDB / ID: 7ogv
TitleA self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine
ComponentsDNA (5'-D(*(P*GP*CP*GP*TP*(DH)P*GP*AP*CP*GP*CP*G-3')
KeywordsDNA / 5-hydroxymethylcitosine / Chemically modified DNA / DNA duplex / Epigenetics
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsBattistini, F. / Dans, P.D. / Terrazas, M. / Castellazzi, C.L. / Portella, G. / Labrador, M. / Villegas, N. / Brun-Heath, I. / Gonzalez, C. / Orozco, M.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2014-61670-EXP Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-89707-P Spain
CitationJournal: Plos Comput.Biol. / Year: 2021
Title: The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.
Authors: Battistini, F. / Dans, P.D. / Terrazas, M. / Castellazzi, C.L. / Portella, G. / Labrador, M. / Villegas, N. / Brun-Heath, I. / Gonzalez, C. / Orozco, M.
History
DepositionMay 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 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 (5'-D(*(P*GP*CP*GP*TP*(DH)P*GP*AP*CP*GP*CP*G-3')
B: DNA (5'-D(*(P*GP*CP*GP*TP*(DH)P*GP*AP*CP*GP*CP*G-3')


Theoretical massNumber of molelcules
Total (without water)7,3892
Polymers7,3892
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1170 Å2
ΔGint-4 kcal/mol
Surface area4670 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1none

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Components

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


Mass: 3694.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY

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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
121isotropic12D DQF-COSY
131isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1 mM DNA (5'-D(*(DC5)P*GP*CP*GP*TP*(DH)P*GP*AP*CP*GP*CP*(DG3))-3'), 90% H2O/10% D2O
Details: buffer: 25 mM sodium phosphate, 100 mM NaCl / Label: unlabelled / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM
Component: DNA (5'-D(*(DC5)P*GP*CP*GP*TP*(DH)P*GP*AP*CP*GP*CP*(DG3))-3')
Isotopic labeling: none
Sample conditionsDetails: 25 mM sodium phosphate, 100 mM NaCl / Ionic strength: 125 mM / Label: conditions_1 / pH: 7.0 Not defined / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: none
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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