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- PDB-1dl4: THE SOLUTION STRUCTURE OF A BAY-REGION 1S-BENZ[A]ANTHRACENE OXIDE... -

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Basic information

Entry
Database: PDB / ID: 1dl4
TitleTHE SOLUTION STRUCTURE OF A BAY-REGION 1S-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE
Components
  • DNA (5'-D(*CP*GP*GP*AP*CP*(BZA)AP*AP*GP*AP*AP*G)-3')
  • DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')
KeywordsDNA / BENZ[A]ANTHRACENE-DNA DUPLEX
Function / homologyChem-BZA / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / NOE-restrained MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsLi, Z. / Kim, H.-Y. / Tamura, P.J. / Harris, C.M. / Harris, T.M. / Stone, M.P.
CitationJournal: Biochemistry / Year: 1999
Title: Intercalation of the (1S,2R,3S,4R)-N6-[1-(1,2,3,4-tetrahydro-2,3, 4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in an oligodeoxynucleotide containing the human N-ras codon 61 sequence.
Authors: Li, Z. / Kim, H.Y. / Tamura, P.J. / Harris, C.M. / Harris, T.M. / Stone, M.P.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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*GP*AP*CP*(BZA)AP*AP*GP*AP*AP*G)-3')
B: DNA (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 / 7structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (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 / Details: THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD
#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: 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
2222D NOESY
3322D NOESY
3422D ROESY
252DQF-COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

Details
Solution-IDContents
11.7 MM OLIGODEOXYNUCLEOTIDE; 10 MM PHOSPHATE BUFFER; 0.05 MM EDTA; 0.1 M NACL
21.7 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 atm283 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 DRXBrukerDRX7501
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2BRUKERcollection
X-PLOR3.851A.BRUNGERstructure 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 477 NOE-DERIVED DISTANCE CONSTRAINTS, 80 EMPIRICAL SUGAR PUCKER RESTRAINTS, 32 BACKBONE ANGLE DIHEDRAL RESTRAINTS, AND 18 EMPIRICAL PLANARITY RESTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 7 / Conformers submitted total number: 1

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