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- PDB-1b3p: 5'-D(*GP*GP*AP*GP*GP*AP*T)-3' -

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Basic information

Entry
Database: PDB / ID: 1b3p
Title5'-D(*GP*GP*AP*GP*GP*AP*T)-3'
ComponentsDNA (5'-D(*GP*GP*AP*GP*GP*AP*T)-3')
KeywordsDNA / (G-G-A) TRIPLET REPEAT / V-SHAPED BACKBONE / PARALLEL-STRANDED SEGMENTS / MISMATCH ALIGNMENTS / UNIFORM 13C / 15N-LABELED DNA
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / distance geometry
AuthorsKettani, A. / Bouaziz, S. / Skripkin, E. / Majumdar, A. / Wang, W. / Jones, R.A. / Patel, D.J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Interlocked mismatch-aligned arrowhead DNA motifs.
Authors: Kettani, A. / Bouaziz, S. / Skripkin, E. / Majumdar, A. / Wang, W. / Jones, R.A. / Patel, D.J.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: 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: DNA (5'-D(*GP*GP*AP*GP*GP*AP*T)-3')
B: DNA (5'-D(*GP*GP*AP*GP*GP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)4,4052
Polymers4,4052
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100ACCEPTABLE COVALENT GEOMETRY, LOW DISTANCE RESTRAINTS VIIOLATIONS AND FAVORABLE NON-BONDED ENERGY VALUES
Representative

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Components

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


Mass: 2202.472 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
14113C-EDITED 13C-PURGED NOESY
15115N-EDITED 15N-PURGED NOESY
161HNN-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR AND HETERONUCLEAR EXPERIMENTS ON 13C AND 15N LABELED SAMPLE. THE DISTANCE RESTRAINTS WERE DEDUCED FROM 5 NOESY MIXING TIMES (50, 100, 150, 200 ...Text: THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR AND HETERONUCLEAR EXPERIMENTS ON 13C AND 15N LABELED SAMPLE. THE DISTANCE RESTRAINTS WERE DEDUCED FROM 5 NOESY MIXING TIMES (50, 100, 150, 200 AND 250 MS) IN D2O AND 2 NOESY MIXING TIMES IN H2O (60 AND 200 MS) MS

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Sample preparation

Sample conditionsIonic strength: 10 mM NACL, 2 mM PHOSPHATE / pH: 6.6 / Pressure: ambient / Temperature: 273 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851BRUNGERstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JNRL CITATION ABOVE
NMR ensembleConformer selection criteria: ACCEPTABLE COVALENT GEOMETRY, LOW DISTANCE RESTRAINTS VIIOLATIONS AND FAVORABLE NON-BONDED ENERGY VALUES
Conformers calculated total number: 100 / Conformers submitted total number: 15

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