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- PDB-1xcz: Structure of DNA containing the beta-anomer of a carbocyclic abas... -

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Basic information

Entry
Database: PDB / ID: 1xcz
TitleStructure of DNA containing the beta-anomer of a carbocyclic abasic site
Components
  • 5'-D(*CP*GP*TP*AP*CP*(DXD)P*CP*AP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*TP*GP*AP*GP*TP*AP*CP*G)-3'
KeywordsDNA / Double helix / abasic site
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Authorsde los Santos, C. / El-khateeb, M. / Rege, P. / Tian, K. / Johnson, F.
CitationJournal: Biochemistry / Year: 2004
Title: Impact of the C1 configuration of abasic sites on DNA duplex structure
Authors: de Los Santos, C. / El-Khateeb, M. / Rege, P. / Tian, K. / Johnson, F.
History
DepositionSep 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / 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_database_remark.text / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Remark 600HETEROGEN Sugar protons identified with asterisks in the coordinate file are named with primes in ...HETEROGEN Sugar protons identified with asterisks in the coordinate file are named with primes in the primary citation.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,5972
Polymers6,5972
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)9 / 20converging structures (<1.5A) and the least restraints violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 3199.103 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Apyrimidinic abasic sites are normally present in all genomes
#2: DNA chain 5'-D(*GP*CP*AP*TP*GP*AP*GP*TP*AP*CP*G)-3'


Mass: 3398.235 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
111COSY, DQF-COSY, COSY45, TOCSY, NOESY, [1H-31P]HETCOR
2222D NOESY
NMR detailsText: Several NOESY spectra recorded using different mixing times.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM sample, 50 mM phosphate buffer, 50 mM NaCl, 1 mM EDTA, 99.96% D2O100% D2O
21.2 mM sample, 50 mM phosphate buffer, 50 mM NaCl, 1 mM EDTA, 90% H2O-10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.9 ambient 290 K
26.9 ambient 277 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-PLOR3.85Brungerrefinement
Felix98Accelrysprocessing
Felix98Accelrysdata analysis
Curves5.1Lavery AND Sklenardata analysis
VNMR6.1Variancollection
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 400 distances between non-exchangeable protons, 26 distance restraints enforcing WC base pairs and 96 backbone dihedral restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: converging structures (<1.5A) and the least restraints violations / Conformers calculated total number: 20 / Conformers submitted total number: 9

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