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- PDB-1ss7: Compensating bends in a 16 base-pair DNA oligomer containing a T3... -

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Basic information

Entry
Database: PDB / ID: 1ss7
TitleCompensating bends in a 16 base-pair DNA oligomer containing a T3A3 segment
Components5'-D(*CP*GP*AP*GP*GP*TP*TP*TP*AP*AP*AP*CP*CP*TP*CP*G)-3'
KeywordsDNA / B-DNA / double helix / Residual dipolar couplings
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / Restrained molecular dynamics
AuthorsMcAteer, K. / Aceves-Gaona, A. / Michalczyk, R. / Buchko, G.W. / Isern, N.G. / Silks, L.A. / Miller, J.H. / Kennedy, M.A.
CitationJournal: Biopolymers / Year: 2004
Title: Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature
Authors: McAteer, K. / Aceves-Gaona, A. / Michalczyk, R. / Buchko, G.W. / Isern, N.G. / Silks, L.A. / Miller, J.H. / Kennedy, M.A.
History
DepositionMar 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 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_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(*CP*GP*AP*GP*GP*TP*TP*TP*AP*AP*AP*CP*CP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*GP*GP*TP*TP*TP*AP*AP*AP*CP*CP*TP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)9,7962
Polymers9,7962
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)15 / 45structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*CP*GP*AP*GP*GP*TP*TP*TP*AP*AP*AP*CP*CP*TP*CP*G)-3'


Mass: 4898.191 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
1112D NOESY
121DQF-COSY
1312D 13C-1H CT-TROSY-HSQC
1412D 15N-1H TROSY-HSQC
NMR detailsText: Heteronuclear dipolar couplings were measured in samples aligned with filamentous Pf1 bacteriophage

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Sample preparation

DetailsContents: 1 mM DNA / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 400 mM NaCl, 40mM phosphate / pH: 7 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

NMR software
NameVersionDeveloperClassification
Felix98MSIprocessing
X-PLOR3.85Brunger, Tjandrarefinement
BIRDER96Zhu, Reiditerative matrix relaxation
RefinementMethod: Restrained molecular dynamics / Software ordinal: 1
Details: Structures are based on a total of 316 NOE, 90 torsion angle, and 6 distance restraints represented each W-C base-pair. For the RDC structures an additional 88 one-bond C-H and 14 one-bond N- ...Details: Structures are based on a total of 316 NOE, 90 torsion angle, and 6 distance restraints represented each W-C base-pair. For the RDC structures an additional 88 one-bond C-H and 14 one-bond N-H residual dipolar coupling restraints were used
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 45 / Conformers submitted total number: 15

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