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- PDB-1qby: THE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE... -

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Basic information

Entry
Database: PDB / ID: 1qby
TitleTHE SOLUTION STRUCTURE OF A BAY-REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE
Components
  • 5'-D(*CP*GP*GP*AP*CP*(BZA)AP*AP*GP*AP*AP*G)-3'
  • 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP* G)-3'
KeywordsDNA / BENZ[A]ANTHRACENE-DNA DUPLEX / INTERCALATION
Function / homologyChem-BZA / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsLi, Z. / Mao, H. / Kim, H.-Y. / Tamura, P.J. / Harris, C.M. / Harris, T.M. / Stone, M.P.
CitationJournal: Biochemistry / Year: 1999
Title: Intercalation of the (-)-(1R,2S,3R, 4S)-N6-[1-benz[a]anthracenyl]-2'-deoxyadenosyl adduct in an oligodeoxynucleotide containing the human N-ras codon 61 sequence.
Authors: Li, Z. / Mao, H. / Kim, H.Y. / Tamura, P.J. / Harris, C.M. / Harris, T.M. / Stone, M.P.
History
DepositionApr 27, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*CP*GP*GP*AP*CP*(BZA)AP*AP*GP*AP*AP*G)-3'
B: 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP* G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9883
Polymers6,7072
Non-polymers2801
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 / 1back calculated data agree with experimental NOESY spectrum
RepresentativeModel #12closest to the average

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Components

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


Mass: 3416.263 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 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: THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD
#3: Chemical ChemComp-BZA / 1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL


Mass: 280.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
322DQF-COSY
332TOCSY
2422D NOESY
NMR detailsText: STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

Details
Solution-IDContents
11.6 MM OLIGODEOXYNUCLEOTIDE; 10 MM PHOSPHATE BUFFER; 0.05 MM EDTA; 0.1 M NACL
21.6 MM OLIGODEOXYNUCLEOTIDE; 10 MM PHOSPHATE BUFFER; 0.05 MM EDTA; 0.1 M NACL
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 M NACL 7.0 1 atm278 K
20.1 M NACL 7.0 1 atm288 K
30.1 M NACL 7.0 1 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AMXBrukerAMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2BRUCKERcollection
X-PLOR3.1BRUNGERstructure solution
Felix97BIOSYM TECHNOLOGIESprocessing
CORMA5.2BORGIAS,B.A., THOMAS,P.D., LI,H., KUMAR,A., AND TONELLI,M.refinement
MARDIGRAS3BORGIAS,B.A., THOMAS,P.D., LI,H., KUMAR,A., AND TONELLI,M.iterative matrix relaxation
RefinementMethod: NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 509 NOE-DERIVED DISTANCE CONSTRAINTS, 95 EMPIRICAL SUGAR PUCKER RESTRAINTS, 36 EMPIRICAL BACKBONE ANGLE DIHEDRAL RESTRAINTS, AND 16 EMPIRICAL PLANARITY RESTRAINTS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 1 / Conformers submitted total number: 1

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