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- PDB-1b4y: STRUCTURE AND MECHANISM OF FORMATION OF THE H-Y5 ISOMER OF AN INT... -

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Entry
Database: PDB / ID: 1b4y
TitleSTRUCTURE AND MECHANISM OF FORMATION OF THE H-Y5 ISOMER OF AN INTRAMOLECULAR DNA TRIPLE HELIX.
ComponentsDNA (H-Y5 TRIPLE HELIX)
KeywordsDNA / H-DNA / TRIPLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsVan Dongen, M.J.P. / Doreleijers, J.F. / Van Der Marel, G.A. / Van Boom, J.H. / Hilbers, C.W. / Wijmenga, S.S.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix.
Authors: van Dongen, M.J. / Doreleijers, J.F. / van der Marel, G.A. / van Boom, J.H. / Hilbers, C.W. / Wijmenga, S.S.
History
DepositionDec 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 23, 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 (H-Y5 TRIPLE HELIX)


Theoretical massNumber of molelcules
Total (without water)9,0731
Polymers9,0731
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)12 / 30LOW ENERGIES
RepresentativeModel #10

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Components

#1: DNA chain DNA (H-Y5 TRIPLE HELIX) / H-DNA


Mass: 9072.822 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE DESIGNED DNA SEQUENCE WAS CHEMICALLY SYNTHESIZED.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121PE-COSY
131TOCSY
14131P-1H
151TOCSY-NOESY

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Sample preparation

DetailsContents: H2O/D2O
Sample conditionsIonic strength: 100 mM / pH: 4.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX 600BrukerAMX 6005001
Varian UNITYPLUSVarianUNITYPLUS6002
Varian UNITYPLUSVarianUNITYPLUS7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.815BRUNGERrefinement
XPLORstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: STRUCTURES WERE OBTAINED BY TORSION ANGLE DYNAMICS, AND SUBSEQUENTLY REFINED BY MEANS OF SIMULATED ANNEALING.
NMR ensembleConformer selection criteria: LOW ENERGIES / Conformers calculated total number: 30 / Conformers submitted total number: 12

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