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- PDB-2hou: Structure ensembles of duplex DNA containing a 4'-oxidized abasic... -

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Basic information

Entry
Database: PDB / ID: 2hou
TitleStructure ensembles of duplex DNA containing a 4'-oxidized abasic site.
Components
  • 5'-D(*CP*CP*AP*AP*AP*GP*(X4A)P*AP*CP*CP*GP*GP*G)-3'
  • 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'
KeywordsDNA / abasic site / DNA lesion / BER / bleomycin
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsChen, J. / Dupradeau, F.Y. / Case, D.A. / Turner, C.J. / Stubbe, J.
CitationJournal: Biochemistry / Year: 2007
Title: Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites.
Authors: Chen, J. / Dupradeau, F.Y. / Case, D.A. / Turner, C.J. / Stubbe, J.
History
DepositionJul 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 8, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Source and taxonomy
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / ndb_struct_conf_na / ndb_struct_na_base_pair / pdbx_entity_src_syn / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _ndb_struct_na_base_pair.buckle / _pdbx_nmr_exptl_sample_conditions.ionic_strength ..._ndb_struct_na_base_pair.buckle / _pdbx_nmr_exptl_sample_conditions.ionic_strength / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Remark 600HETEROGEN X4A IS AN ALPHA ANOMER. THEREFORE, C1' CENTER HAS CORRECT CHIRALITY AT X4A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*CP*AP*AP*AP*GP*(X4A)P*AP*CP*CP*GP*GP*G)-3'
B: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,8522
Polymers7,8522
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1570 Å2
ΔGint-4 kcal/mol
Surface area5150 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain 5'-D(*CP*CP*AP*AP*AP*GP*(X4A)P*AP*CP*CP*GP*GP*G)-3'


Mass: 3893.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: strand containing 4'-oxidized abasic site / Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'


Mass: 3958.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template strand / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131E-COSY
141PE-COSY
151GE-HSQC
161PH-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.0 mM duplex DNA containing a 4'-oxidized abasic site, 10 mM sodium phosphate, 0.2 EDTA mM, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution22.0 mM duplex DNA containing a 4'-oxidized abasic site, 10 mM sodium phosphate, 0.2 EDTA mM, 100% D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMduplex DNA containing a 4'-oxidized abasic sitenatural abundance1
2.0 mMduplex DNA containing a 4'-oxidized abasic sitenatural abundance2
10 mMsodium phosphatenatural abundance1
10 mMsodium phosphatenatural abundance2
0.2 mMEDTAnatural abundance1
0.2 mMEDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mM sodium phosphate mMsample_conditions_16.5 1 atm298 K
210 mM sodium phosphate mMsample_conditions_26.5 1 atm277 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built Home builtHome-builtHome built7501
Home-built Home builtHome-builtHome built5912

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Processing

NMR software
NameVersionDeveloperClassification
Amber8D.A. Case et alrefinement
FELIX2001data analysis
MARDIGRASdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on 410 NOE-derived distance constraints and 43 dihedral angle restraints,8 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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