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- PDB-2m54: Refined NMR solution structure of metal-modified DNA -

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Basic information

Entry
Database: PDB / ID: 2m54
TitleRefined NMR 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
Function / homologySILVER ION / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKumbhar, S. / Johannsen, S. / Sigel, R.K. / Waller, M.P. / Mueller, J.
CitationJournal: J.Inorg.Biochem. / Year: 2013
Title: A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.
Authors: Kumbhar, S. / Johannsen, S. / Sigel, R.K. / Waller, M.P. / Muller, J.
History
DepositionFeb 13, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
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

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 ds DNA, 0.9-1.5 mM SILVER ION, 120 mM sodium perchlorate, 100% D2O100% D2O
20.3-0.5 mM ds DNA, 0.9-1.5 mM SILVER ION, 120 mM sodium perchlorate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentConc. range (mg/ml)Solution-ID
mMds DNA-10.3-0.51
mMSILVER ION-20.9-1.51
120 mMsodium perchlorate-31
mMds DNA-40.3-0.52
mMSILVER ION-50.9-1.52
120 mMsodium perchlorate-62
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 AvanceBrukerAVANCE4002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3, 2.0, 2.1Bruker Biospinprocessing
Sparky3.1Goddardchemical shift assignment
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 constraintsNA alpha-angle constraints total count: 34 / NA beta-angle constraints total count: 34 / NA chi-angle constraints total count: 28 / NA delta-angle constraints total count: 28 / NA epsilon-angle constraints total count: 34 / NA gamma-angle constraints total count: 34 / NA other-angle constraints total count: 0 / NOE 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 / Hydrogen bond constraints total count: 56
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

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