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- PDB-229d: DNA ANALOG OF YEAST TRANSFER RNA PHE ANTICODON DOMAIN WITH MODIFI... -

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Basic information

Entry
Database: PDB / ID: 229d
TitleDNA ANALOG OF YEAST TRANSFER RNA PHE ANTICODON DOMAIN WITH MODIFIED BASES 5-METHYL CYTOSINE AND 1-METHYL GUANINE
ComponentsDNA (5'-D(*CP*CP*AP*GP*AP*CP*(UMP)P*GP*AP*AP*(MG1)P*AP*(UMP)P*(5CM)P*(UMP)P*GP*G)-3')
KeywordsDNA / TRANSFER RNA / ANTICODON / HAIRPIN LOOP
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsBasti, M.M. / Stuart, J.W. / Lam, A.T. / Guenther, R. / Agris, P.F.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA(Phe) anticodon domain.
Authors: Basti, M.M. / Stuart, J.W. / Lam, A.T. / Guenther, R. / Agris, P.F.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Direct Observation of Two Base-Pairing Modes of a Cytosine-Thymine Analogue with Guanine in a DNA Z-Form Duplex: Significance for Base Analogue Mutagenesis
Authors: Moore, M.H. / Van Meervelt, L. / Salisbury, S.A. / Lin, P.K.T. / Brown, D.M.
History
DepositionAug 16, 1995Processing site: BNL
Revision 1.0Dec 7, 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

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*GP*AP*CP*(UMP)P*GP*AP*AP*(MG1)P*AP*(UMP)P*(5CM)P*(UMP)P*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,2221
Polymers5,2221
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(*CP*CP*AP*GP*AP*CP*(UMP)P*GP*AP*AP*(MG1)P*AP*(UMP)P*(5CM)P*(UMP)P*GP*G)-3')


Mass: 5222.388 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

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Processing

NMR softwareName: Discover / Developer: BIOSYM TECHNOLOGIES / Classification: refinement
RefinementSoftware ordinal: 1
Details: NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 537 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE SOLUTION STRUCTURE OF THE 17-MER DNA ...Details: NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 537 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE SOLUTION STRUCTURE OF THE 17-MER DNA HAIRPIN LOOP WAS DETERMINED BASED ON 246 DISTANCE AND DIHEDRAL RESTRAINTS ESTIMATED FROM 2D NOE SPECTRUM. TEN LOW ENERGY STRUCTURES WERE USED TO GENERATE THIS AVERAGE STRUCTURE WHICH WAS FURTHER ENERGY MINIMIZED.
NMR ensembleConformers submitted total number: 1

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