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- PDB-1s0t: Solution structure of a DNA duplex containing an alpha-anomeric a... -

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Basic information

Entry
Database: PDB / ID: 1s0t
TitleSolution structure of a DNA duplex containing an alpha-anomeric adenosine: insights into substrate recognition by endonuclease IV
Components
  • 5'-D(*Cp*Gp*Tp*Cp*Gp*Tp*Gp*Gp*Ap*C)-3'
  • 5'-D(*Gp*Tp*Cp*Cp*(A3A)p*Cp*Gp*Ap*Cp*G)-3'
KeywordsDNA / DNA double helix with enlarged miner groove and helical kink
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics molecular dynamics
Model type detailsminimized average
AuthorsAramini, J.M. / Cleaver, S.H. / Pon, R.T. / Cunningham, R.P. / Germann, M.W.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution Structure of a DNA Duplex Containing an alpha-Anomeric Adenosine: Insights into Substrate Recognition by Endonuclease IV.
Authors: Aramini, J.M. / Cleaver, S.H. / Pon, R.T. / Cunningham, R.P. / Germann, M.W.
History
DepositionJan 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 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(*Gp*Tp*Cp*Cp*(A3A)p*Cp*Gp*Ap*Cp*G)-3'
B: 5'-D(*Cp*Gp*Tp*Cp*Gp*Tp*Gp*Gp*Ap*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0912
Polymers6,0912
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 / 10
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain 5'-D(*Gp*Tp*Cp*Cp*(A3A)p*Cp*Gp*Ap*Cp*G)-3'


Mass: 3029.994 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The core of the sequence corresponds to the recognition site of E. coli endonuclease IV
#2: DNA chain 5'-D(*Cp*Gp*Tp*Cp*Gp*Tp*Gp*Gp*Ap*C)-3'


Mass: 3061.003 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 NOESY
121DQF-COSY
1312D TOCSY
1412D 31P,1H correlation
151HSQC
NMR detailsText: For non-exchangeable protons, NOESY experiments in D2O were performed with 10s relaxation delays and mixing times of 75ms, 150ms and 250 ms. For exchangeable protons, a WATERGATE NOESY was ...Text: For non-exchangeable protons, NOESY experiments in D2O were performed with 10s relaxation delays and mixing times of 75ms, 150ms and 250 ms. For exchangeable protons, a WATERGATE NOESY was performed with a relaxation delay of 4s and 150ms mixing time.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6100% D2O
21.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.690% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl 6.6ambient 293 K
250 mM NaCl 6.6ambient 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert et alrefinement
Amber6Case et al.refinement
MARDIGRAS3.2Borgias et al.iterative matrix relaxation
CORMA5.2Keepers and Jamesstructure solution
Curves5.1Lavery and Sklenarstructure solution
MOLMOL2Koradi et al.structure solution
RefinementMethod: torsion angle dynamics molecular dynamics / Software ordinal: 1
Details: The structure is based on a total of 502 restraints: 284 distance restraints, 80 endocyclic torsion angle restraints, 50 Watson-Crick distance and angle restraints, and 88 backbone torsion ...Details: The structure is based on a total of 502 restraints: 284 distance restraints, 80 endocyclic torsion angle restraints, 50 Watson-Crick distance and angle restraints, and 88 backbone torsion angle restraints. The alphaA duplex structure was elucidated by a combination of DYANA and rMD/rEM in AMBER. All calculations were performed in vacuo. The final structure deposited here was obtained by coordinate averaging the final ensemble of 10 rMD/rEM structures followed by restrained energy minimization.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers calculated total number: 10 / Conformers submitted total number: 1

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