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- PDB-2z2g: NMR Structure of the IQ-modified Dodecamer CTC[IQ]GGCGCCATC -

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Basic information

Entry
Database: PDB / ID: 2z2g
TitleNMR Structure of the IQ-modified Dodecamer CTC[IQ]GGCGCCATC
Components
  • DNA (5'-D(*DCP*DTP*DCP*DGP*DGP*DCP*DGP*DCP*DCP*DAP*DTP*DC)-3')
  • DNA (5'-D(*DGP*DAP*DTP*DGP*DGP*DCP*DGP*DCP*DCP*DGP*DAP*DG)-3')
KeywordsDNA / Nar1IQ1 / rMD calculations / NOESY / COSY / Refinement / IQ / Adduct
Function / homology3-METHYL-3H-IMIDAZO[4,5-F]QUINOLIN-2-AMINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing restrained molecular dynamics
AuthorsWang, F. / Elmquist, C.E. / Stover, J.S. / Rizzo, C.J. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2007
Title: DNA sequence modulates the conformation of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme
Authors: Wang, F. / Elmquist, C.E. / Stover, J.S. / Rizzo, C.J. / Stone, M.P.
History
DepositionMay 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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
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
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_database_related / pdbx_entity_src_syn
Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*DCP*DTP*DCP*DGP*DGP*DCP*DGP*DCP*DCP*DAP*DTP*DC)-3')
B: DNA (5'-D(*DGP*DAP*DTP*DGP*DGP*DCP*DGP*DCP*DCP*DGP*DAP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5263
Polymers7,3282
Non-polymers1981
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 12structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-D(*DCP*DTP*DCP*DGP*DGP*DCP*DGP*DCP*DCP*DAP*DTP*DC)-3')


Mass: 3599.343 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The unmodified oligodeoxynucleotide 5'-d(GATGGCGCCGAG)-3' was obtained from the Midland Certified Reagent Company, and had been purified by anion exchange chromatography. The IQ-adducted ...Details: The unmodified oligodeoxynucleotide 5'-d(GATGGCGCCGAG)-3' was obtained from the Midland Certified Reagent Company, and had been purified by anion exchange chromatography. The IQ-adducted oligodeoxynucleotides 5'-d(CTCXGCGCCATC)-3' and 5'-d(CTCGXCGCCATC)-3' were synthesized and purified as described in paper by Elmquist, C. Eric.[J. Am. Chem. Soc., Vol. 126, No. 36, 2004].
Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*DGP*DAP*DTP*DGP*DGP*DCP*DGP*DCP*DCP*DGP*DAP*DG)-3')


Mass: 3728.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GIQ / 3-METHYL-3H-IMIDAZO[4,5-F]QUINOLIN-2-AMINE / 2-AMINO-3-METHYLIMIDAZO[4,5-F]QUINOLINE


Mass: 198.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D NOESY
221Magnitude COSY
331E-COSY
341DQF-COSY
351P-COSY
1622D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM modified duplex, 10mM phosphate buffer with 0.1M NaCl and 0.05mM Na2EDTA (pH 7.0), D2O10mM phosphate buffer with 0.1M NaCl and 0.05mM Na2EDTA (pH 7.0), D2O
20.7mM modified duplex, 10mM phosphate buffer with 0.1M NaCl and 0.05mM Na2EDTA (pH 7.0), 90% H2O and 10% D2O10mM phosphate buffer with 0.1M NaCl and 0.05mM Na2EDTA (pH 7.0), 90% H2O and 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1M NaCl 7.0 1 atm278 K
20.1M NaCl 7.0 1 atm288 K
30.1M NaCl 7.0 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker TXIBrukerTXI8001
Bruker QXIBrukerQXI6002
Bruker TXIBrukerTXI5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerrefinement
Felix95Biosym/MSIprocessing
MARDIGRAS5.2Borgiasiterative matrix relaxation
CORMA5.2Keepersiterative matrix relaxation
RefinementMethod: simulated annealing restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 12 / Conformers submitted total number: 10

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