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- PDB-2ke8: NMR solution structure of metal-modified DNA -

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Basic information

Entry
Database: PDB / ID: 2ke8
TitleNMR solution structure of metal-modified DNA
ComponentsDNA (5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3')
KeywordsDNA / artificial nucleobase / imidazole nucleoside / Ag+
Function / homologySILVER ION / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJohannsen, S. / Duepre, N. / Boehme, D. / Mueller, J. / Sigel, R.K.O.
CitationJournal: Nat.Chem. / Year: 2010
Title: Solution structure of a DNA double helix with consecutive metal-mediated base pairs.
Authors: Johannsen, S. / Megger, N. / Bohme, D. / Sigel, R.K. / Muller, J.
History
DepositionJan 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3')
B: DNA (5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3545
Polymers10,0312
Non-polymers3243
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33)P*AP*AP*AP*TP*TP*AP*A)-3')


Mass: 5015.311 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ag

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-13C HSQC
1412D 1H-15N HSQC
1511D 31P
2622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-0.5 mM DNA (34-MER)-1, 120 mM sodium perchlorate-2, 0.9-1.5 mM SILVER ION-3, 100% D2O100% D2O
20.3-0.5 mM DNA (34-MER)-4, 120 mM sodium perchlorate-5, 0.9-1.5 mM SILVER ION-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mMDNA (34-MER)-10.3-0.51
120 mMsodium perchlorate-21
mMSILVER ION-30.9-1.51
mMDNA (34-MER)-40.3-0.52
120 mMsodium perchlorate-52
mMSILVER ION-60.9-1.52
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.127.2ambient 298 K
20.127.2ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AV 2BrukerAV 24002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3, 2.0, 2.1Bruker Biospinprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddarddata analysis
Sparky3.1Goddardpeak picking
DYANA1.5Guntert, Braun and Wuthrichstructure solution
X-PLOR NIH2.15Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.15Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 848 / NOE intraresidue total count: 366 / NOE long range total count: 15 / NOE medium range total count: 25 / NOE sequential total count: 442
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.2 Å
NMR ensemble rmsDistance rms dev: 1.06 Å / Distance rms dev error: 0.34 Å

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