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- PDB-1agk: THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-... -

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Basic information

Entry
Database: PDB / ID: 1agk
TitleTHE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE
Components
  • DNA (5'-D(*CP*GP*GP*AP*CP*RP*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 / R-STYRENE OXIDE ADDUCT / N6-ADENINE / MAJOR GROOVE / DEOXYRIBONUCLEIC ACID
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsFeng, B. / Stone, M.P.
Citation
Journal: Biochemistry / Year: 1995
Title: Major groove (R)-alpha-(N6-adenyl)styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 61 sequence: conformations of the R(61,2) and R(61,3) sequence isomers from 1H NMR.
Authors: Feng, B. / Zhou, L. / Passarelli, M. / Harris, C.M. / Harris, T.M. / Stone, M.P.
#1: Journal: 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 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: database_2 / entity_poly ...database_2 / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _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 2.1May 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*GP*AP*CP*RP*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)6,8282
Polymers6,8282
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*RP*AP*GP*AP*AP*G)-3')


Mass: 3536.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: (R)-(N6-ADENYL)-STYRENE OXIDE-RAS61-2 DNA ADDUCT
#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: (R)-(N6-ADENYL)-STYRENE OXIDE-RAS61-2 DNA ADDUCT

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212QF-COSY
131AND TOCSY
141: NOESY
1512QF-COSY
161AND(DO
17105'-D

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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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