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- PDB-1yct: Clustered abasic lesions in dna: nmr solution structure of cluste... -

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Basic information

Entry
Database: PDB / ID: 1yct
TitleClustered abasic lesions in dna: nmr solution structure of clustered bistranded +1 abasic lesion
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*CP*CP*AP*TP*GP*CP*G)-3'
KeywordsDNA / DOUBLE HELIX / ABASIC SITES / CLUSTERED DAMAGE / EXTRUDED RESIDUES / REDUCED AP SITE / FURAN / BISTRANDED ABASIC LESION.
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsHazel, R.D. / de los Santos, C.
CitationJournal: Biochemistry / Year: 2008
Title: NMR solution structures of bistranded abasic site lesions in DNA.
Authors: Hazel, R.D. / Tian, K. / de Los Santos, C.
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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*CP*CP*AP*TP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,6872
Polymers7,6872
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)5 / 20structures with the least restraint violations
RepresentativeModel #1closest to the average

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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*CP*CP*AP*TP*GP*CP*G)-3'


Mass: 3843.488 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
1212D TOCSY
131DQF-COSY
141COSY, COSY45
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM DUPLEX, 25 mM PHOSPHATE BUFFER, 50 mM NaCl, 0.5 mM EDTA.
Solvent system: 25 mM PHOSPHATE BUFFER, PH 6.8; 50 mM NaCl; 0.5 mM EDTA.
Sample conditionsIonic strength: NOT DETERMINED / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1A. BRUNGERrefinement
FELIX98processing
INSIGHT95data analysis
MIDAS PLUSdata analysis
CURVES5data analysis
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: 1) HEATING STAGE: FROM 150 TO 500 K IN 70PS. INTRODUCTION OF EXPERIMENTAL RESTRAINTS AT THE END OF THIS STAGE. 2) HIGH TEMPERATURE STAGE: 50 PS DYNAMICS AT 500K 3) COOLING STAGE: FROM 500 TO ...Details: 1) HEATING STAGE: FROM 150 TO 500 K IN 70PS. INTRODUCTION OF EXPERIMENTAL RESTRAINTS AT THE END OF THIS STAGE. 2) HIGH TEMPERATURE STAGE: 50 PS DYNAMICS AT 500K 3) COOLING STAGE: FROM 500 TO 300K IN 40PS. 4) EQUILIBRATION STAGE: 120PS DYNAMICS AT 300K
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 5

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