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- PDB-1ht7: STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE LESIO... -

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Basic information

Entry
Database: PDB / ID: 1ht7
TitleSTRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE LESION STAGGERED IN A 5'-ORIENTATION.
Components
  • 5'-D(*CP*GP*CP*AP*TP*GP*(3DR)P*GP*TP*AP*CP*GP*C)-3'
  • 5'-D(*GP*CP*GP*TP*AP*(3DR)P*AP*CP*AP*TP*GP*CP*G)-3'
KeywordsDNA / double helix / abasic sites / clustered damage / extruded residues.
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / Restrained molecular dynamics
AuthorsLin, Z. / de los Santos, C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: NMR characterization of clustered bistrand abasic site lesions: effect of orientation on their solution structure.
Authors: Lin, Z. / de los Santos, C.
History
DepositionDec 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: 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 / 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
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*CP*AP*TP*GP*(3DR)P*GP*TP*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*(3DR)P*AP*CP*AP*TP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,7112
Polymers7,7112
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)6 / 30structures with the least restraint violations
Representative

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Components

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


Mass: 3843.488 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Randomly designed sequence containing stable abasic sites (3DR).
#2: DNA chain 5'-D(*GP*CP*GP*TP*AP*(3DR)P*AP*CP*AP*TP*GP*CP*G)-3'


Mass: 3867.513 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Randomly designed sequence containing stable abasic sites (3DR).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121COSY, COSY45, TOCSY, DQFCOSY, HETCOR
2322D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA.99.96% D2O
22mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA.90% H2O/10% D2O (v/v)
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1not determined 7.6 ambient 298 K
2not determined 7.6 ambient 276 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix98MSIprocessing
MARDIGRAS5Borgia & Jamesdata analysis
X-PLOR3.1A. Brungerrefinement
Insight95MSIdata analysis
MidasPlusUCSFdata analysis
Curves5Sklenar & Laverydata analysis
RefinementMethod: Restrained molecular dynamics / Software ordinal: 1
Details: 1) Heating stage: from 100 to 500 K in 4ps. Introduction of experimental restraints at the end of this stage. 2) High temperature stage: 80 ps dynamics at 500K 3) Cooling stage: From 500 to ...Details: 1) Heating stage: from 100 to 500 K in 4ps. Introduction of experimental restraints at the end of this stage. 2) High temperature stage: 80 ps dynamics at 500K 3) Cooling stage: From 500 to 300K in 40ps. 4) Equilibration stage: 140ps dynamics at 300K.
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 6

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