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- PDB-2hkc: NMR Structure of the IQ-modified Dodecamer CTCGGC[IQ]GCCATC -

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Basic information

Entry
Database: PDB / ID: 2hkc
TitleNMR Structure of the IQ-modified Dodecamer CTCGGC[IQ]GCCATC
Components
  • 5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3'
  • 5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'
KeywordsDNA / Nar1IQ3 / rMD calculations / Anneal / NOESY / COSY / Refinement / IQ / Adduct / HCA
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. / DeMuro, N.E. / Elmquist, C.E. / Stover, J.S. / Rizzo, C.J. / Stone, M.P.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions.
Authors: Wang, F. / DeMuro, N.E. / Elmquist, C.E. / Stover, J.S. / Rizzo, C.J. / Stone, M.P.
History
DepositionJul 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Source and taxonomy
Category: database_2 / diffrn ...database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_sample_details / 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_ensemble.conformer_selection_criteria / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.authors / _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 29, 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(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3'
B: 5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5263
Polymers7,3282
Non-polymers1981
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 12structures with the lowest energy
RepresentativeModel #1closest to the average structure

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Components

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


Mass: 3599.343 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The unmodified oligodeoxynucleotides 5'-d(CTCGGCGCCATC)-3' and 5'-d(GATGGCGCCGAG)-3' were obtained from the Midland Certified Reagent Company, and had been purified by anion exchange ...Details: The unmodified oligodeoxynucleotides 5'-d(CTCGGCGCCATC)-3' and 5'-d(GATGGCGCCGAG)-3' were obtained from the Midland Certified Reagent Company, and had been purified by anion exchange chromatography. The IQ-adducted oligodeoxynucleotide 5'-d(CTCGGCXCCATC)-3' was 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 5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-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
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM modified duplex, 10 mM phosphate buffer, 0.1 M NaCl, 0.05 mM Na2EDTA, 100% D2Osample_1100% D2O
solution20.7 mM modified duplex, 10 mM phosphate buffer, 0.1 M NaCl, 0.05 mM Na2EDTA, 90% H2O/10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMmodified duplexnatural abundance1
10 mMphosphate buffernatural abundance1
0.1 mMNaClnatural abundance1
0.05 mMNa2EDTAnatural abundance1
0.7 mMmodified duplexnatural abundance2
10 mMphosphate buffernatural abundance2
0.1 mMNaClnatural abundance2
0.05 mMNa2EDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.1 M NaCl Not definedconditions_17.0 Not defined1 atm278 K
20.1 M NaCl Not definedconditions_27.0 Not defined1 atm288 K
30.1 M NaCl Not definedconditions_37.0 Not defined1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerrefinement
Felix95Accelrys Software Inc.processing
MARDIGRAS5.2Borgiasiterative matrix relaxation
CORMA5.2Keepersiterative matrix relaxation
RefinementMethod: simulated annealing restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 12 / Conformers submitted total number: 8

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