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- PDB-2m11: Structure of perimidinone-derived synthetic nucleoside paired wit... -

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Basic information

Entry
Database: PDB / ID: 2m11
TitleStructure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(D3N)P*GP*CP*G)-3')
KeywordsDNA / B-form DNA / dPer / Perimidinone-Derived Nucleoside / Dickerson-Drew Dodecamer
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsmean structure, model1
Model type detailsminimized average
AuthorsKowal, E.A. / Lad, R. / Pallan, P.S. / Muffly, E. / Wawrzak, Z. / Egli, M. / Sturla, S.J. / Stone, M.P.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.
Authors: Kowal, E.A. / Lad, R.R. / Pallan, P.S. / Dhummakupt, E. / Wawrzak, Z. / Egli, M. / Sturla, S.J. / Stone, M.P.
History
DepositionNov 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3May 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
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_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_comp_id / _struct_conn.ptnr2_label_seq_id

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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*AP*AP*TP*TP*(D3N)P*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(D3N)P*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,4732
Polymers7,4732
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(D3N)P*GP*CP*G)-3')


Mass: 3736.484 Da / Num. of mol.: 2 / Source method: obtained synthetically

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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 COSY
2322D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate, 100% D2O100% D2O
20.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 10 mM sodium phosphate, 50 uM EDTA, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.53 mM5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3'-11
100 mMsodium chloride-21
50 uMEDTA-31
10 mMsodium phosphate-41
0.53 mM5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3'-52
10 mMsodium phosphate-62
50 uMEDTA-72
100 mMsodium chloride-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 7.0 ambient 283 K
2100 7.0 ambient 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CORMAThomas L. Jamesdata analysis
Curves5.3Ravishankar, G. et al.data analysis
MARDIGRASThomas L. Jamesprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 153
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 10

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