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- PDB-2rt8: Structure of metallo-dna in solution -

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Basic information

Entry
Database: PDB / ID: 2rt8
TitleStructure of metallo-dna in solution
Components
  • DNA (5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / METALLO-BASE-PAIR / T-HG(II)-T BASE-PAIR
Function / homology: / DNA
Function and homology information
MethodSOLUTION NMR / SIMMULATED ANNEALING
Model detailslowest energy, model 1
AuthorsYamaguchi, H. / Sebera, J. / Kondo, J. / Oda, S. / Komuro, T. / Kawamura, T. / Dairaku, T. / Kondo, Y. / Okamoto, I. / Ono, A. ...Yamaguchi, H. / Sebera, J. / Kondo, J. / Oda, S. / Komuro, T. / Kawamura, T. / Dairaku, T. / Kondo, Y. / Okamoto, I. / Ono, A. / Burda, J.V. / Kojima, C. / Sychrovsky, V. / Tanaka, Y.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation.
Authors: Yamaguchi, H. / Sebera, J. / Kondo, J. / Oda, S. / Komuro, T. / Kawamura, T. / Dairaku, T. / Kondo, Y. / Okamoto, I. / Ono, A. / Burda, J.V. / Kojima, C. / Sychrovsky, V. / Tanaka, Y.
History
DepositionJun 18, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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_atom_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,4744
Polymers6,0732
Non-polymers4012
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3011.966 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3')


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-HG / MERCURY (II) ION / 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-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1312D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0 mM 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'-1, 2.0 mM 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'-2, 4.0 mM Mercury(II) perchlorate-3, 100 mM Sodium perchlorate-4, 100 % [U-100% 2H] D2O-5, 100% D2O100% D2O
22.0 mM 5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'-6, 2.0 mM 5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'-7, 4.0 mM Mercury(II) perchlorate-8, 100 mM Sodium perchlorate-9, 95 % H2O-10, 5 % [U-100% 2H] D2O-11, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mM5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'-11
2.0 mM5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'-21
4.0 mMMercury(II) perchlorate-31
100 mMSodium perchlorate-41
100 %D2O-5[U-100% 2H]1
2.0 mM5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'-62
2.0 mM5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'-72
4.0 mMMercury(II) perchlorate-82
100 mMSodium perchlorate-92
95 %H2O-102
5 %D2O-11[U-100% 2H]2
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometerType: BRUKER DRX800 / Manufacturer: Bruker / Model: DRX800 / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851structure solution
X-PLOR3.851refinement
Sparky3.1Goddardprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddardpeak picking
MARDIGRASThomas L. Jamesstructure solution
RefinementMethod: SIMMULATED ANNEALING / Software ordinal: 1
NMR constraintsNOE constraints total: 628
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 17 / Representative conformer: 1

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