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- PDB-1hz0: NMR STRUCTURE OF THE 2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRID... -

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Basic information

Entry
Database: PDB / ID: 1hz0
TitleNMR STRUCTURE OF THE 2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE (PHIP) C8-DEOXYGUANOSINE ADDUCT IN DUPLEX DNA
Components
  • DNA (5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3')
KeywordsDNA / DNA adduct duplex
Function / homology2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained torsion angle minimizations
AuthorsBrown, K. / Cosman, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Solution structure of the 2-amino-1- methyl-6-phenylimidazo[4,5-b]pyridine C8-deoxyguanosine adduct in duplex DNA.
Authors: Brown, K. / Hingerty, B.E. / Guenther, E.A. / Krishnan, V.V. / Broyde, S. / Turteltaub, K.W. / Cosman, M.
History
DepositionJan 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_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
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*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3')
B: DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9333
Polymers6,7082
Non-polymers2241
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 48structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3254.138 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA oligomers synthesized on an ABI 394 DNA/RNA synthesizer and chemically modified by N-acetoxy-PhIP
#2: DNA chain DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3')


Mass: 3454.258 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-PIQ / 2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE


Mass: 224.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
3322D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
19.1 mg of [PhIP]dG.dC 11mer duplex in 600 ul of 10 mM Na2PO4 buffer100% D2O
29.1 mg of [PhIP]dG.dC 11mer duplex in 600 ul of 10 mM Na2PO4 buffer90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 M NaCl 7ambient 298 K
20.1 M NaCl 7ambient 293 K
30.1 M NaCl 7ambient 274 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6Variancollection
Felix97MSIdata analysis
DUPLEXnoneHingerty and Broydestructure solution
DUPLEXnoneHingerty and Broyderefinement
RefinementMethod: restrained torsion angle minimizations / Software ordinal: 1
Details: A total of 266 NOE-derived distance constraints were used in the calculations
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 48 / Conformers submitted total number: 6

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