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- PDB-1s75: SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING AN ALPHA-ANOMERIC A... -

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Basic information

Entry
Database: PDB / ID: 1s75
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 28, 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 / -
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
15113C,1H HSQC
161
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
MARDIGRAS3.2Borgias et al.structure solution
CORMA5.2Keepers and Jamesstructure solution
Curves5.1Lavery and Sklenarstructure solution
MOLMOL2Koradi et al.structure solution
Amber6.1Case et al.refinement
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. THE IN VACUO STRUCTURE WAS THEN SOLVATED IN A SOLVENT BOX AND NA+ COUNTERIONS. THE FOLLOWING SIMULATIONS CONTAINED 25 C-H RESIDUAL DIPOLAR COUPLINGS RESTRAINTS. THE FINAL SOLVATED STRUCTURE WAS OBTAINED BY AVERAGING THE LAST 5PS OF A 1 NS RMD RUN FOLLOWED BY REM.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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