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- PDB-214d: THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-M... -

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Basic information

Entry
Database: PDB / ID: 214d
TitleTHE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT
Components
  • DNA (5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*TP*AP*(T41)P*AP*TP*GP*CP*G)-3')
KeywordsDNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsGotfredsen, C.H. / Spielmann, H.P. / Wengel, J. / Jacobsen, J.P.
CitationJournal: Bioconjug.Chem. / Year: 1996
Title: Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement.
Authors: Gotfredsen, C.H. / Spielmann, H.P. / Wengel, J. / Jacobsen, J.P.
History
DepositionJul 7, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: 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_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_database_status.process_site / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 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(*CP*GP*CP*AP*TP*AP*TP*AP*GP*CP*C)-3')
B: DNA (5'-D(*GP*GP*CP*TP*AP*(T41)P*AP*TP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,7372
Polymers6,7372
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 40all calculated structures submitted
Representative

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*GP*CP*C)-3') / 2'-OCH3-ARAT DNA / TAXA


Mass: 3318.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: DNA chain DNA (5'-D(*GP*GP*CP*TP*AP*(T41)P*AP*TP*GP*CP*G)-3') / 2'-OCH3-ARAT DNA / TAXA


Mass: 3419.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionClassification
MARDIGRASrefinement
Discover2.9.5refinement
RefinementMethod: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1
Details: REFINEMENT WAS BASED ON TOTAL RELAXATION MATRIX ANALYSIS OF THE NOESY CROSS PEAK INTENSITIES USING THE PROGRAM MARDIGRAS. IMPROVED PROCEDURES TO CONSIDER THE EXPERIMENTAL "NOISE" IN NOESY ...Details: REFINEMENT WAS BASED ON TOTAL RELAXATION MATRIX ANALYSIS OF THE NOESY CROSS PEAK INTENSITIES USING THE PROGRAM MARDIGRAS. IMPROVED PROCEDURES TO CONSIDER THE EXPERIMENTAL "NOISE" IN NOESY SPECTRA DURING THESE CALCULATIONS HAVE BEEN EMPLOYED (H.LIU, H.P.SPIELMANN, D.E.WEMMER, AND T.L.JAMES (1995) IN PREPARATION). THE NOE-DERIVED DISTANCE RESTRAINTS WERE APPLIED IN RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WITH AMBER FORCEFIELD POTENTIALS AS IMPLEMENTED IN DISCOVER. THE ROOT-MEAN-SQUARE (RMS) DEVIATION OF THE COORDINATES FOR THE FORTY STRUCTURES OF THE DUPLEX WAS 0.82 ANGSTROMS.
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 40 / Conformers submitted total number: 40

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