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- PDB-1d19: SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUC... -

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Entry
Database: PDB / ID: 1d19
TitleSOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED REFINEMENT
ComponentsDNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3')
KeywordsDNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / ENERGY MINIMIZATION, MOLECULAR DYNAMICS
AuthorsBaleja, J.D. / Sykes, B.D.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement.
Authors: Baleja, J.D. / Germann, M.W. / van de Sande, J.H. / Sykes, B.D.
#1: Journal: J.Magn.Reson. / Year: 1990
Title: Distance Measurement and Structure Refinement with Noe Data
Authors: Baleja, J.D. / Moult, J. / Sykes, B.D.
History
DepositionAug 1, 1990Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,8532
Polymers4,8532
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)1 / -
Representative

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Components

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


Mass: 2426.617 Da / Num. of mol.: 2 / 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

NMR softwareName: GROMOS / Developer: DE VLIEG ET AL. / Classification: refinement
RefinementMethod: ENERGY MINIMIZATION, MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE STRUCTURE WAS THEN REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.19 OVER ALL OBSERVED, QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE USED TO REFINE THESE STRUCTURES ...Details: THE STRUCTURE WAS THEN REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.19 OVER ALL OBSERVED, QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE USED TO REFINE THESE STRUCTURES INCLUDED CORRELATION TIME ADJUSTMENT FACTORS, WHICH ARE APPROXIMATELY RELATED TO THE INVERSE OF THE TEMPERATURE FACTORS ASSOCIATED WITH X-RAY CRYSTALLOGRAPHY. THESE VALUES ARE INCLUDED IN THE COLUMN NORMALLY USED FOR TEMPERATURE FACTORS. VALUES OF 0.0 APPEAR FOR NON-HYDROGEN ATOMS, WHICH WERE NOT USED IN THE NMR CALCULATIONS. FURTHER DETAILS ARE GIVEN IN REFERENCE 1.
NMR ensembleConformers submitted total number: 1

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