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- PDB-6fy6: Concerted dynamics of metallo-base pairs in an A/B-form helical t... -

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Basic information

Entry
Database: PDB / ID: 6fy6
TitleConcerted dynamics of metallo-base pairs in an A/B-form helical transition (major species)
ComponentsDNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_major
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')_major
B: DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_major
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 the binding site.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1660 Å2
ΔGint-64 kcal/mol
Surface area5140 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')_major


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
363isotropic12D 1H-1H NOESY
323isotropic12D 1H-1H COSY
333isotropic12D 1H-1H TOCSY
373isotropic12D 1H-13C HSQC aliphatic
383isotropic12D 1H-13C HSQC aromatic
242isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution20.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 90% H2O/10% D2O1_H2O/D2O90% H2O/10% D2O
solution30.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 100% D2O1_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMpolydeoxyribonucleotidenone2
1.2 mMMERCURY (II) IONnone2
0.4 mMpolydeoxyribonucleotidenone3
1.2 mMMERCURY (II) IONnone3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
250 mMconditions_27.75ambient atm277 K
350 mMconditions_37.35 pDambient atm298 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
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
SparkyGoddardpeak picking
Xplor-NIH2.46G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandrarefinement
RefinementMethod: simulated annealing / Software ordinal: 5
Details: 2000 preliminary structures were calculated. The 20 lowest energy structures were selected and subsequently refined. Of the 200 refined conformers calculated 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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