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- PDB-1ir5: Solution Structure of the 17mer TF1 Binding Site -

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Basic information

Entry
Database: PDB / ID: 1ir5
TitleSolution Structure of the 17mer TF1 Binding Site
Components
  • 5'-D(*CP*AP*CP*TP*AP*CP*AP*AP*AP*GP*AP*GP*TP*AP*GP*TP*G)-3'
  • 5'-D(*CP*AP*CP*TP*AP*CP*TP*CP*TP*TP*TP*GP*TP*AP*GP*TP*G)-3'
KeywordsDNA / 17mer double helix DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, W. / Vu, H.M. / Kearns, D.R.
CitationJournal: ACTA BIOCHIM.BIOPHYS.SINICA / Year: 2002
Title: 1H NMR studies of a 17-mer DNA duplex
Authors: Liu, W. / Vu, H.M. / Kearns, D.R.
History
DepositionSep 7, 2001Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: 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 1.4Dec 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: 5'-D(*CP*AP*CP*TP*AP*CP*TP*CP*TP*TP*TP*GP*TP*AP*GP*TP*G)-3'
B: 5'-D(*CP*AP*CP*TP*AP*CP*AP*AP*AP*GP*AP*GP*TP*AP*GP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)10,4132
Polymers10,4132
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)20 / 20all calculated structures submitted
RepresentativeModel #1

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Components

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


Mass: 5168.357 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Bacillus Subtilis phage SPO1
#2: DNA chain 5'-D(*CP*AP*CP*TP*AP*CP*AP*AP*AP*GP*AP*GP*TP*AP*GP*TP*G)-3'


Mass: 5244.438 Da / Num. of mol.: 1 / 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
222DQF-COSY
3332D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 2mM DNA, 100mM phosphate buffer, 90% H2O, 10% D2O
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: Discover / Version: 3.1 / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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