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- PDB-7bfs: deoxyxylose nucleic acid hairpin -

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Basic information

Entry
Database: PDB / ID: 7bfs
Titledeoxyxylose nucleic acid hairpin
ComponentsDNA (5'-D(*AP*GP*CP*AP*AP*TP*CP*CP*(XC)P*(XC)P*(XC)P*(XC)P*GP*GP*AP*TP*TP*GP*CP*T)-3')
KeywordsDNA / deoxyxylose nucleic acid / chimeric
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsMattelaer, C.-A. / Mohitosh, M. / Smets, L. / Maiti, M. / Schepers, G. / Mattelaer, H.-P. / Rosemeyer, H. / Herdewijn, P. / Lescrinier, E.
Funding support Belgium, 2items
OrganizationGrant numberCountry
KU LeuvenC14/29/102 Belgium
Research Foundation - Flanders (FWO)1S23217N Belgium
CitationJournal: Chembiochem / Year: 2021
Title: Stable Hairpin Structures Formed by Xylose-Based Nucleic Acids.
Authors: Mattelaer, C.A. / Maiti, M. / Smets, L. / Maiti, M. / Schepers, G. / Mattelaer, H.P. / Rosemeyer, H. / Herdewijn, P. / Lescrinier, E.
History
DepositionJan 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*CP*AP*AP*TP*CP*CP*(XC)P*(XC)P*(XC)P*(XC)P*GP*GP*AP*TP*TP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)6,0631
Polymers6,0631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3910 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-D(*AP*GP*CP*AP*AP*TP*CP*CP*(XC)P*(XC)P*(XC)P*(XC)P*GP*GP*AP*TP*TP*GP*CP*T)-3')


Mass: 6062.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cruciform ColE1 / Source: (synth.) Escherichia coli (E. coli)
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: anisotropic / Type: 2D NOESY

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Sample preparation

DetailsType: solution / Contents: 2.9 mM oligomer, 100% D2O / Label: D2O / Solvent system: 100% D2O
SampleConc.: 2.9 mM / Component: oligomer / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 M / Label: 1 / pH: 6.6 pD / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 5 / Details: explicit solvent
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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