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- PDB-1agh: THE SOLUTION STRUCTURE OF AN 11 BASE-PAIR OLIGONUCLEOTIDE DUPLEX ... -

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Entry
Database: PDB / ID: 1agh
TitleTHE SOLUTION STRUCTURE OF AN 11 BASE-PAIR OLIGONUCLEOTIDE DUPLEX CODING FOR AMINO ACIDS 60-62 OF THE PRODUCT OF THE N-RAS PROTOONCOGENE, NMR, MINIMIZED AVERAGE STRUCTURE
Components
  • DNA (5'-D(*CP*GP*GP*AP*CP*AP*AP*GP*AP*AP*G)-3')
  • DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')
KeywordsDNA / DNA DUPLEX / B-DNA / HUMAN N-RAS GENE / CODON 61 SEQUENCE / DEOXYRIBONUCLEIC ACID
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsFeng, B. / Stone, M.P.
CitationJournal: Chem.Res.Toxicol. / Year: 1995
Title: Solution structure of an oligodeoxynucleotide containing the human n-ras codon 61 sequence refined from 1H NMR using molecular dynamics restrained by nuclear Overhauser effects.
Authors: Feng, B. / Stone, M.P.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: 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
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
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*GP*GP*AP*CP*AP*AP*GP*AP*AP*G)-3')
B: DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,7072
Polymers6,7072
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 / 1THIS STRUCTURE PROVIDED THE BEST-FIT FOR THE NOE DATA BASED ON THE RELAXATION MATRIX ANALYSIS USING CORMA.
Representative

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Components

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


Mass: 3416.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HUMAN N-RAS PROTOONCOGENE
#2: DNA chain DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')


Mass: 3291.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HUMAN N-RAS PROTOONCOGENE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212QF-COSY
131TOCSY

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Sample preparation

Sample conditionspH: 6.9 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Felixstructure solution
X-PLORstructure solution
MARDIGRASstructure solution
CORMAstructure solution
RefinementMethod: NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: THIS STRUCTURE PROVIDED THE BEST-FIT FOR THE NOE DATA BASED ON THE RELAXATION MATRIX ANALYSIS USING CORMA.
Conformers calculated total number: 1 / Conformers submitted total number: 1

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