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- PDB-1hx4: MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS DETERMINES ... -

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Basic information

Entry
Database: PDB / ID: 1hx4
TitleMOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS DETERMINES DNA ADDUCT CONFORMATION: A LINK TO TUMORIGENIC ACTIVITY
Components
  • 5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3'
  • 5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3'
KeywordsDNA / 1R-trans-anti-BPh-N2-G adduct / carcinogen-dna adduct / benzo[c]phenanthrene dna adduct
Function / homologyChem-BPJ / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, relaxation matrix refinements, energe minimization
AuthorsPatel, D.J. / Lin, C.H. / Geacintov, N.E. / Broyde, S. / Huang, X. / Kolbanovskii, A. / Hingerty, B.E. / Amin, S.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Molecular topology of polycyclic aromatic carcinogens determines DNA adduct conformation: a link to tumorigenic activity.
Authors: Lin, C.H. / Huang, X. / Kolbanovskii, A. / Hingerty, B.E. / Amin, S. / Broyde, S. / Geacintov, N.E. / Patel, D.J.
History
DepositionJan 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,9893
Polymers6,7082
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)9 / 9structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: DNA chain 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: Synthesized from ABI-DNA Synthesizer
#2: DNA chain 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 / Details: Synthesized from ABI-DNA Synthesizer
#3: Chemical ChemComp-BPJ / (1R)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4-TRIOL / 1R-TRANS-ANTI-BENZO[C]PHENANTHRENE


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
121P-COSY
1311H-31P HSQC
NMR detailsText: D2O NMR experiments were performed at 13 degree C, H2O NMR experiments were performed at 4 degree C

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Sample preparation

DetailsContents: 1R-trans-anti-BPh (carcinogen) covalently bound to 11mer DNA duplex
Solvent system: aqueous solution
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: 1 atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA4003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Associates Inc.processing
Felixfelix2000MSIdata analysis
X-PLOR3.1Brunger, A. T.refinement
RefinementMethod: torsion angle dynamics, simulated annealing, relaxation matrix refinements, energe minimization
Software ordinal: 1
Details: Nonexchangeable interproton distance restraints were obtained from the buildup of NOE cross peak volumes in NOESY data sets (55, 100, 150 and 200 ms mixing times) on the 1S-(-)-trans-anti- ...Details: Nonexchangeable interproton distance restraints were obtained from the buildup of NOE cross peak volumes in NOESY data sets (55, 100, 150 and 200 ms mixing times) on the 1S-(-)-trans-anti-(BPh)G*C and the 1R-(+)-trans-anti-(BPh)G*C 11-mer DNA duplex adducts in D2O buffer at 23 and 18 sC, respectively, and bounds were set between 15% and 25% of the calculated distances using the fixed cytidine H5-H6 reference distance of 2.45 . Non-stereospecific assignments were treated with r-6 averaging. Interproton distance restraints involving exchangeable protons of the same complex were obtained from NOESY spectra (90 and 150 ms mixing times) in H2O buffer at 4 sC with bounds set between 20% and 25% of the calculated distance using the thymine imino to adenine H2 reference distance of 2.91 across an A*T base pair.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 9 / Conformers submitted total number: 9

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