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- PDB-1dgo: SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA -

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Basic information

Entry
Database: PDB / ID: 1dgo
TitleSOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA
ComponentsURACIL CONTAINING HAIRPIN DNA
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. / Kumar, N.V. / Varshney, U. / Chary, K.V.R.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: Structural basis for uracil DNA glycosylase interaction with uracil: NMR study.
Authors: Ghosh, M. / Vinay Kumar, N. / Varshney, U. / Chary, K.V.
History
DepositionNov 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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: URACIL CONTAINING HAIRPIN DNA


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)9 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1zero violations and lowest energy

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Components

#1: DNA chain URACIL CONTAINING HAIRPIN DNA


Mass: 5483.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Custom made by 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 standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
15 mM oligo; no buffer; pH = 7.0 Temp = 305K; 99% D2O99% D2O
25 mM oligo; no buffer; pH = 7.0 Temp = 305K; 90% H20 +10% D2O90% H20 +10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
171 atm305 K
271 atm295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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 a total of 225 restraints, 145 are NOE-derived distance constraints, 64 dihedral aangle restraints, 16 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: zero violations and 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: 9

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