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- PDB-1n4b: Solution Structure of the undecamer CGAAAC*TTTCG -

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Basic information

Entry
Database: PDB / ID: 1n4b
TitleSolution Structure of the undecamer CGAAAC*TTTCG
Components
  • 5'-D(*CP*GP*AP*AP*AP*CP*TP*TP*TP*CP*G)-3'
  • 5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3'
KeywordsDNA / interstrand cross-link / alkylated DNA / modified cytosine / alkylated cytosine
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsWebba da Silva, M. / Noronha, A.M. / Noll, D.M. / Miller, P.S. / Colvin, O.M. / Gamcsik, M.P.
CitationJournal: Biochemistry / Year: 2002
Title: Solution Structure of a DNA Duplex Containing Mispair-Aligned N4C-Ethyl-N4C Interstrand Cross-Linked Cytosines
Authors: Webba da Silva, M. / Noronha, A.M. / Noll, D.M. / Miller, P.S. / Colvin, O.M. / Gamcsik, M.P.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 25, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*GP*AP*AP*AP*CP*TP*TP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,6942
Polymers6,6942
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 / 100the structure submitted is the lowest energy structure of a an ensemble of selected ten structures
RepresentativeModel #1closest to the average,lowest energy

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Components

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


Mass: 3333.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interstrand Cross-Linked DNA
#2: DNA chain 5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3'


Mass: 3361.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interstrand Cross-Linked DNA

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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
1422D NOESY

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Sample preparation

DetailsContents: The synthesis by solid phase methods of DNA duplexes that contain an N4-C-ethyl-N4C interstrand cross-link has been described [Biochemistry,41(2002)760-771]. 2 mM single strand ...Contents: The synthesis by solid phase methods of DNA duplexes that contain an N4-C-ethyl-N4C interstrand cross-link has been described [Biochemistry,41(2002)760-771]. 2 mM single strand concentration in 0.3 mL containing 10 mM sodium phosphate (pH 7.4) and 100 mM NaCl.
Solvent system: both 1H2O (95%) and 2H2O (5%), and 99.9 % 2H2O.
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 7.4normal 293 K
2100 mM NaCl 7.4normal 273 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Varian INOVAVarianINOVA5003

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Processing

NMR softwareName: X-PLOR / Version: 3.8 / Developer: Brunger, A.T. / Classification: refinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
Details: A total of 449 restraints were used 243 non-exchangeable 53 exchangeable 44 hydrogen bond 109 dihedral angle
NMR representativeSelection criteria: closest to the average,lowest energy
NMR ensembleConformer selection criteria: the structure submitted is the lowest energy structure of a an ensemble of selected ten structures
Conformers calculated total number: 100 / Conformers submitted total number: 1

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