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- PDB-1dau: Analog of dickerson-drew DNA dodecamer with 6'-alpha-methyl carbo... -

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Basic information

Entry
Database: PDB / ID: 1dau
TitleAnalog of dickerson-drew DNA dodecamer with 6'-alpha-methyl carbocyclic thymidines, NMR, minimized average structure
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*(T32)P*(T32)P*CP*GP*CP*G)-3')
KeywordsDNA / CARBOCYCLIC / DODECAMER / DEOXYRIBONUCLEIC ACID / MINIMIZED AVERAGE STRUCTURE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MD
AuthorsDenisov, A. / Bekiroglu, S. / Maltseva, T. / Sandstrom, A. / Altmann, K.-H. / Egli, M. / Chattopadhyaya, J.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1998
Title: The solution conformation of a carbocyclic analog of the Dickerson-Drew dodecamer: comparison with its own X-ray structure and that of the NMR structure of the native counterpart.
Authors: Denisov, A.Y. / Zamaratski, E.V. / Maltseva, T.V. / Sandstrom, A. / Bekiroglu, S. / Altmann, K.H. / Egli, M. / Chattopadhyaya, J.
History
DepositionJan 21, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: 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: 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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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*GP*AP*AP*(T32)P*(T32)P*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(T32)P*(T32)P*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3752
Polymers7,3752
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 / 9LOWEST ENERGY, BEST AGREEMENT WITH NOE VOLUMES
Representative

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*(T32)P*(T32)P*CP*GP*CP*G)-3')


Mass: 3687.500 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
111NOESY
121DQF-COSY

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Sample preparation

Sample conditionspH: 7.0 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX 600 / Manufacturer: Bruker / Model: DRX 600 / Field strength: 600 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionDeveloperClassification
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
AURELIAstructure solution
Amberstructure solution
MARDIGRASstructure solution
RefinementMethod: RESTRAINED MD / Software ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN THE PAPER.
NMR ensembleConformer selection criteria: LOWEST ENERGY, BEST AGREEMENT WITH NOE VOLUMES
Conformers calculated total number: 9 / Conformers submitted total number: 1

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