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- PDB-2rmq: Solution structure of fully modified 4'-thioDNA with the sequence... -

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Basic information

Entry
Database: PDB / ID: 2rmq
TitleSolution structure of fully modified 4'-thioDNA with the sequence of d(CGCGAATTCGCG)
ComponentsDNA (5'-D(*(C4S)P*(S4G)P*(C4S)P*(S4G)P*(S4A)P*(S4A)P*(T49)P*(T49)P*(C4S)P*(S4G)P*(C4S)P*(S4G))-3')
KeywordsDNA / 4'-thioDNA / A-form
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsMatsugami, A. / Ohyama, T. / Inada, M. / Katahira, M.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance
Authors: Matsugami, A. / Ohyama, T. / Inada, M. / Inoue, N. / Minakawa, N. / Matsuda, A. / Katahira, M.
History
DepositionNov 12, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_leaving_atom_flag
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*(C4S)P*(S4G)P*(C4S)P*(S4G)P*(S4A)P*(S4A)P*(T49)P*(T49)P*(C4S)P*(S4G)P*(C4S)P*(S4G))-3')
B: DNA (5'-D(*(C4S)P*(S4G)P*(C4S)P*(S4G)P*(S4A)P*(S4A)P*(T49)P*(T49)P*(C4S)P*(S4G)P*(C4S)P*(S4G))-3')


Theoretical massNumber of molelcules
Total (without water)7,7122
Polymers7,7122
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)1 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*(C4S)P*(S4G)P*(C4S)P*(S4G)P*(S4A)P*(S4A)P*(T49)P*(T49)P*(C4S)P*(S4G)P*(C4S)P*(S4G))-3')


Mass: 3856.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D DQF-COSY
2222D 1H-1H TOCSY
2322D 1H-1H NOESY
2422D 1H-1H NOESY
2522D 1H-13C HSQC
1612D 1H-1H NOESY
1712D 1H-1H NOESY
1812D 1H-13C JR-HMBC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.42mM 4'-thio DNA; 10mM sodium phosphate; 10mM sodium chloride; 0.01mM DSS; 95% H2O, 5% D2O95% H2O/5% D2O
20.42mM 4'-thio DNA; 10mM sodium phosphate; 10mM sodium chloride; 0.01mM DSS; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.42 mM4'-thio DNA1
10 mMsodium phosphate1
10 mMsodium chloride1
0.01 mMDSS1
0.42 mM4'-thio DNA2
10 mMsodium phosphate2
10 mMsodium chloride2
0.01 mMDSS2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 6.5 ambient 278 K
220 6.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
TopSpin1Bruker Biospincollection
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDraw2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.111Goddarddata analysis
Sparky3.111Goddardpeak picking
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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