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- PDB-1s37: Accomodation of Mispair-Aligned N3T-Ethyl-N3T DNA Interstrand Cro... -

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Basic information

Entry
Database: PDB / ID: 1s37
TitleAccomodation of Mispair-Aligned N3T-Ethyl-N3T DNA Interstrand Crosslink
Components
  • DNA (5'-D(*CP*GP*AP*AP*AP*(TTM)P*TP*TP*TP*CP*G)-3')
  • DNA (5'-D(*CP*GP*AP*AP*AP*TP*TP*TP*TP*CP*G)-3')
KeywordsDNA / interstrand crosslink / DNA interstrand cross-link
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
Model type detailsminimized average
Authorsda Silva, M.W. / Noronha, A.M. / Noll, D.M. / Miller, P.S. / Colvin, O.M. / Gamcsik, M.P.
CitationJournal: Biochemistry / Year: 2004
Title: Accommodation of mispair aligned N3T-ethyl-N3T DNA interstrand cross link.
Authors: da Silva, M.W. / Wilds, C.J. / Noronha, A.M. / Colvin, O.M. / Miller, P.S. / Gamcsik, M.P.
History
DepositionJan 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 30, 2014Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*AP*AP*AP*(TTM)P*TP*TP*TP*CP*G)-3')
B: DNA (5'-D(*CP*GP*AP*AP*AP*TP*TP*TP*TP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,7242
Polymers6,7242
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)1 / 8structures with the lowest energy
RepresentativeModel #8minimized average structure

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Components

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


Mass: 3376.263 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*AP*AP*AP*TP*TP*TP*TP*CP*G)-3')


Mass: 3348.209 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
1212D TOCSY
131DQF-COSY
NMR detailsText: Structure Determined using standard NMR experiments.

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Sample preparation

DetailsContents: 100 mM NaCl, pH 7.4 adjusted with phosphate buffer
Solvent system: H2O, D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 mM NaCl 7.4 normal 273 K
20.1 mM NaCl 7.4 normal 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000data analysis
X-PLOR3.2A.T. Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 8 / Conformers submitted total number: 1

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