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- PDB-6fy7: Concerted dynamics of metallo-base pairs in an A/B-form helical t... -

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Basic information

Entry
Database: PDB / ID: 6fy7
TitleConcerted dynamics of metallo-base pairs in an A/B-form helical transition (minor species)
ComponentsDNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_minor
KeywordsDNA / metallated duplex DNA / B-form helix / A-form helix / mercury(II)-mediated base pair
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsSchmidt, O.P. / Jurt, S. / Johannsen, S. / Karimi, A. / Sigel, R.K.O. / Luedtke, N.W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation165949 Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: Concerted dynamics of metallo-base pairs in an A/B-form helical transition.
Authors: Schmidt, O.P. / Jurt, S. / Johannsen, S. / Karimi, A. / Sigel, R.K.O. / Luedtke, N.W.
History
DepositionMar 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,9134
Polymers8,5122
Non-polymers4012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: We performed CD spectroscopy and concentration dependant thermal melting temperature experiments to confirm formation of B-form duplex DNA. We used site-selective 15N-labeling and 199Hg- ...Evidence: We performed CD spectroscopy and concentration dependant thermal melting temperature experiments to confirm formation of B-form duplex DNA. We used site-selective 15N-labeling and 199Hg-enriched Hg(ClO4)2 to determine binding site.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1680 Å2
ΔGint-62 kcal/mol
Surface area5220 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

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


Mass: 4255.778 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
313isotropic22D 1H-1H NOESY
323isotropic12D 1H-1H COSY
333isotropic12D 1H-1H TOCSY
343isotropic12D 1H-13C HSQC aliphatic
353isotropic12D 1H-13C HSQC aromatic

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Sample preparation

DetailsType: solution
Contents: 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 100% D2O
Label: 1_D2O / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMpolydeoxyribonucleotidenone3
1.2 mMMERCURY (II) IONnone3
Sample conditionsIonic strength: 50 mM / Label: conditions_3 / pH: 7.35 pD / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardpeak picking
Xplor-NIH2.46G. Marius Clore, Guillermo Bermejo, John Kuszewski, Charles D. Schwieters, and Nico Tjandrarefinement
TopSpin4.0.0.b.16Bruker Biospincollection
Xplor-NIH2.46G. Marius Clore, Guillermo Bermejo, John Kuszewski, Charles D. Schwieters, and Nico Tjandrastructure calculation
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 2
Details: 2000 preliminary structures were calculated. The 20 lowest energy structures were subsequently refined. From the 200 calculated refined conformers the 20 lowest energy structures were chosen
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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