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- PDB-2mo2: Solution NMR structure of DNA dodecamer containing the 5-hydroxyc... -

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Basic information

Entry
Database: PDB / ID: 2mo2
TitleSolution NMR structure of DNA dodecamer containing the 5-hydroxycytosine
ComponentsDNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5OC)P*GP*CP*G)-3')
KeywordsDNA / 5-hydroxycytosine
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsDonahue, P.S. / Szulik, M.W. / Stone, M.P.
CitationJournal: To be Published
Title: Characterization of 5-hydroxycytosine in DNA
Authors: Szulik, M.
History
DepositionApr 17, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1May 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5OC)P*GP*CP*G)-3')
B: DNA_(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5OC)P*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3592
Polymers7,3592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1509 Å2
ΔGint-11 kcal/mol
Surface area4868 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 40back 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*(5OC)P*GP*CP*G)-3')


Mass: 3679.392 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

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Sample preparation

DetailsContents: 100 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5OC)P*GP*CP*G)-3'), 100 % D2O, 10 mM sodium phosphate, 100 mM sodium chloride, 11 mM sodium azide, 0.05 mM EDTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5OC)P*GP*CP*G)-3')-11
100 %D2O-21
10 mMsodium phosphate-31
100 mMsodium chloride-41
11 mMsodium azide-51
0.05 mMEDTA-61
Sample conditionspH: 7 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker INOVA / Manufacturer: Bruker / Model: INOVA / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 40 / Conformers submitted total number: 11

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