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- PDB-2mmq: Solution structure of AGT FAPY Modified duplex -

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Basic information

Entry
Database: PDB / ID: 2mmq
TitleSolution structure of AGT FAPY Modified duplex
Components
  • DNA_(5'-D(*CP*TP*AP*AP*(FAG)P*TP*TP*TP*CP*A)-3')
  • DNA_(5'-D(*TP*GP*AP*AP*AP*CP*TP*TP*AP*G)-3')
KeywordsDNA / Aflatoxin B1 / FAPY / FORMAMIDOPYRIMIDINE / INTERCALATION / DNA ADDUCT / DEOXYRIBONUCLEIC ACID / HYDROGEN BOND / SEQUENCE DEPENDENCE / AGT
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model1
AuthorsLi, L. / Stone, M.
CitationJournal: Chem.Res.Toxicol. / Year: 2015
Title: DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct.
Authors: Li, L. / Brown, K.L. / Ma, R. / Stone, M.P.
History
DepositionMar 17, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA_(5'-D(*CP*TP*AP*AP*(FAG)P*TP*TP*TP*CP*A)-3')
B: DNA_(5'-D(*TP*GP*AP*AP*AP*CP*TP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,4332
Polymers6,4332
Non-polymers00
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 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA_(5'-D(*CP*TP*AP*AP*(FAG)P*TP*TP*TP*CP*A)-3')


Mass: 3365.292 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA_(5'-D(*TP*GP*AP*AP*AP*CP*TP*TP*AP*G)-3')


Mass: 3068.042 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.5 mM DNA (5'-D(*CP*TP*AP*AP*(FAG)P*TP*TP*TP*CP*A)-3'), 0.5 mM DNA (5'-D(*TP*GP*AP*AP*AP*CP*TP*TP*AP*G)-3'), 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMDNA (5'-D(*CP*TP*AP*AP*(FAG)P*TP*TP*TP*CP*A)-3')-11
0.5 mMDNA (5'-D(*TP*GP*AP*AP*AP*CP*TP*TP*AP*G)-3')-21
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.115Goddardchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
Amber12Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 1

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