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- PDB-2n9f: Glucose as non natural nucleobase -

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Basic information

Entry
Database: PDB / ID: 2n9f
TitleGlucose as non natural nucleobase
Components
  • DNA (5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3')
  • DNA (5'-D(*GP*AP*TP*GP*AP*CP*(4JA)P*GP*CP*TP*AP*G)-3')
KeywordsDNA / Carbohydrate-DNA interaction / carbohydrate nucleobase
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsGomez-Pinto, I. / Vengut-Climent, E. / Lucas, R. / Avino, A. / Eritja, R. / Gonzalez-Ibanez, C. / Morales, J. / Penalver, P. / Fonseca-Guerra, C. / Bickelhaupt, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA.
Authors: Vengut-Climent, E. / Gomez-Pinto, I. / Lucas, R. / Penalver, P. / Avino, A. / Fonseca Guerra, C. / Bickelhaupt, F.M. / Eritja, R. / Gonzalez, C. / Morales, J.C.
History
DepositionNov 20, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: chem_comp / pdbx_entity_src_syn ...chem_comp / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jun 14, 2023Group: Database references / Other / Structure summary / Category: chem_comp / database_2 / pdbx_database_status
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3')
B: DNA (5'-D(*GP*AP*TP*GP*AP*CP*(4JA)P*GP*CP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3372
Polymers7,3372
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)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*AP*TP*GP*AP*CP*(4JA)P*GP*CP*TP*AP*G)-3')


Mass: 3698.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1412D 1H-1H COSY
NMR detailsText: The structure was determined using NOE data

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Sample preparation

DetailsContents: 1 mM DNA (5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3'), 1 mM DNA (5'-D(*GP*AP*TP*GP*AP*CP*(GL6)P*GP*CP*TP*AP*G)-3'), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMDNA (5'-D(*CP*TP*AP*GP*CP*GP*GP*TP*CP*AP*TP*C)-3')-11
1 mMDNA (5'-D(*GP*AP*TP*GP*AP*CP*(GL6)P*GP*CP*TP*AP*G)-3')-21
Sample conditionsIonic strength: Potassium phosphate / pH: 7 / Pressure: ambient / Temperature: 279.6 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanchemical shift assignment
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanprocessing
AmberGoddardrefinement
AmberGoddardchemical shift assignment
AmberGoddardprocessing
AmberBruker Biospinrefinement
AmberBruker Biospinchemical shift assignment
AmberBruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 265 / NOE intraresidue total count: 131 / NOE long range total count: 16 / NOE medium range total count: 235 / NOE sequential total count: 104
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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