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- PDB-1laq: Solution Structure of the B-DNA Duplex CGCGGTXTCCGCG (X=PdG) Cont... -

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Basic information

Entry
Database: PDB / ID: 1laq
TitleSolution Structure of the B-DNA Duplex CGCGGTXTCCGCG (X=PdG) Containing the 1,N2-propanodeoxyguanosine Adduct with the Deoxyribose at C20 Opposite PdG in the C2' Endo Conformation.
Components
  • 5'-D(*CP*GP*CP*GP*GP*AP*(DNR)P*AP*CP*CP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*GP*GP*TP*(P)P*TP*CP*CP*GP*CP*G)-3'
KeywordsDNA / B-type / propanodeoxyguanosine
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / Molecular dynamics using a simulated annealing protocol.
Model type detailsminimized average
AuthorsWeisenseel, J.P. / Reddy, G.R. / Marnett, L.J. / Stone, M.P.
CitationJournal: Chem.Res.Toxicol. / Year: 2002
Title: Structure of an oligodeoxynucleotide containing a 1,N(2)-propanodeoxyguanosine adduct positioned in a palindrome derived from the Salmonella typhimurium hisD3052 gene: Hoogsteen pairing at pH 5.2.
Authors: Weisenseel, J.P. / Reddy, G.R. / Marnett, L.J. / Stone, M.P.
History
DepositionMar 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: database_2 / entity_poly ...database_2 / entity_poly / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _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: 5'-D(*CP*GP*CP*GP*GP*TP*(P)P*TP*CP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*GP*AP*(DNR)P*AP*CP*CP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,9882
Polymers7,9882
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

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


Mass: 4024.636 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This Synthetic DNA sequence was derived from the hisD3052 gene of salmonella typhimurium.
#2: DNA chain 5'-D(*CP*GP*CP*GP*GP*AP*(DNR)P*AP*CP*CP*GP*CP*G)-3'


Mass: 3963.584 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This Synthetic DNA sequence was derived from the hisD3052 gene of salmonella typhimurium.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
13131P-1H COSY
2422D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM DNA strand, 10 mM sodium phosphate, 100 mM NaCl, 50 uM EDTAD2O
21.8 mM DNA strand, 1 mM sodium phosphate, 100 mM NaCl, 50 uM EDTAH2O/D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 5.2 ambient 303 K
2100 mM NaCl 5.2 ambient 278 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: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR3Brukercollection
Felix97.0, 2000Hare, D.data analysis
MARDIGRAS3.2Borgias & Jamesiterative matrix relaxation
X-PLOR3.8Brunger, A.refinement
RefinementMethod: Molecular dynamics using a simulated annealing protocol.
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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