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- PDB-1ii1: Structural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study -

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Basic information

Entry
Database: PDB / ID: 1ii1
TitleStructural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study
Components5'-D(*AP*GP*GP*AP*TP*CP*CP*UP*TP*TP*TP*GP*GP*AP*TP*CP*CP*T)-3'
KeywordsDNA / Uracil / Hairpin DNA / Hairpin loop / Double helix / UDG-Uracil interaction
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics, energy minimization
AuthorsGhosh, M. / Rumpal, N. / Varshney, U. / Chary, K.V.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Structural basis for poor uracil excision from hairpin DNA. An NMR study.
Authors: Ghosh, M. / Rumpal, N. / Varshney, U. / Chary, K.V.
History
DepositionApr 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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(*AP*GP*GP*AP*TP*CP*CP*UP*TP*TP*TP*GP*GP*AP*TP*CP*CP*T)-3'


Theoretical massNumber of molelcules
Total (without water)5,4841
Polymers5,4841
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 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

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


Mass: 5483.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Custom made Ransom Hill Biosciences, Inc., Ramona CA (USA)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121E-COSY
2322D NOESY
NMR detailsText: This structure was determined using 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM oligo; no buffer; pH = 7.0; 305K; 99% D2O99% D2O
22 mM oligo; no buffer; pH = 7.0; 305K; 90% H2O + 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
171 atm305 K
271 atm295 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
Varian UNITYPLUSVarianUNITYPLUS6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
Discover97MSIstructure solution
VNMR6.1Variandata analysis
UXNMR3Brukercollection
Felix97MSIprocessing
Felix97MSIdata analysis
Discover97MSIrefinement
RefinementMethod: restrained molecular dynamics, energy minimization / Software ordinal: 1
Details: The structures are based on total of 227 restraints, 143 are NOE-derived distance constraints, 64 dihedral angle restraints, 10 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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