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- PDB-1n1n: Structure of Mispairing of the Deoxycytosine with Deoxyadenosine ... -

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Basic information

Entry
Database: PDB / ID: 1n1n
TitleStructure of Mispairing of the Deoxycytosine with Deoxyadenosine 5' to the 8,9-Dihydro-8-(N7-guanyl)-9-Hydroxy-Aflatoxin B1 Adduct
Components
  • 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'
  • 5'-D(*AP*GP*AP*TP*CP*AP*AP*TP*GP*T)-3'
KeywordsDNA / Aflatoxin B1 adduct 5' to AC mismatch / Major conformation
Function / homology8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 / DNA
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing NMR data : Felix 97, 2000 molecular dynamics : XPLOR, AMBER matrix relaxation CORMA torsion angle dynamics Gaussian 98, INSIGHTII (2000)
Model type detailsminimized average
AuthorsStone, M.P. / Giri, I.
CitationJournal: Biochemistry / Year: 2003
Title: Wobble dC.dA pairing 5' to the cationic guanine N7 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 adduct: implications for nontargeted AFB1 mutagenesis.
Authors: Giri, I. / Stone, M.P.
History
DepositionOct 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'
B: 5'-D(*AP*GP*AP*TP*CP*AP*AP*TP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4023
Polymers6,0722
Non-polymers3301
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 / 20
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'


Mass: 3003.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: engineered Synthetic Oligo Nulceotide
#2: DNA chain 5'-D(*AP*GP*AP*TP*CP*AP*AP*TP*GP*T)-3'


Mass: 3068.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Oligo Nulceotide
#3: Chemical ChemComp-AFN / 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1


Mass: 330.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131P-COSY
2422D NOESY
3532D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
1the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer for NMR containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2The sample was dissolved in 99.96% D2O.
2the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 6.7 for NMR studiesThe sample was dissolved in 99.96% D2O.
3the ample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2 for NMR studiesthe sample was dissolved in 9:1 H2O:D2O.
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA 7.2 ambient 278 K
20.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA 6.7 ambient 278 K
30.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA 7.2 ambient 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR6.5Brungerrefinement
Insight II2000Accelaris Incstructure solution
Felix97, 2000Accelaris INCdata analysis
MARDIGRAS5.2, 6.2Borgias, B. A., & James, T. L.iterative matrix relaxation
Amber6Caserefinement
XwinNMR3Bruker Inccollection
RefinementMethod: distance geometry simulated annealing NMR data : Felix 97, 2000 molecular dynamics : XPLOR, AMBER matrix relaxation CORMA torsion angle dynamics Gaussian 98, INSIGHTII (2000)
Software ordinal: 1
Details: Distance was calculated using RANDMARDI protocol from MARDIGRAS. The 20 structures obtained from molecular dynamics simulation using X-PLOR starting from random, and B-starting structures. ...Details: Distance was calculated using RANDMARDI protocol from MARDIGRAS. The 20 structures obtained from molecular dynamics simulation using X-PLOR starting from random, and B-starting structures. The final structure emerged from average of 20 simulated annealing structure from B-form starting structure. The average structure was solvated using X-LEAP protocol in AMBER 6.0, and subjected to 1.4 ns MD simulation using AMBER 6.0 SANDER module, in presence of counter IONs. The final structure was obtained by energy minimization of simulated structure. Solvent, and counter ions were omitted. Back Calculations were performed using CORMA.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers calculated total number: 20 / Conformers submitted total number: 1

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