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- PDB-1a9i: APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, ALPHA FORM... -

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Basic information

Entry
Database: PDB / ID: 1a9i
TitleAPYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, ALPHA FORM, NMR, 1 STRUCTURE
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AABP*AP*CP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3')
KeywordsDNA / DAMAGED DNA / APYRIMIDINIC DNA / WATER
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / matrix relaxation
AuthorsBeger, R.D. / Bolton, P.H.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Structures of apurinic and apyrimidinic sites in duplex DNAs.
Authors: Beger, R.D. / Bolton, P.H.
History
DepositionApr 6, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 9, 2014Group: Structure summary
Revision 1.4Apr 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,6012
Polymers6,6012
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100AVERAGE OF 5 STRUCTURES THAT THE NOESY BACKCALCULATION AGREES WITH EXPERIMENTAL NOESY
Representative

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Components

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


Mass: 3211.077 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*CP*GP*TP*AP*TP*CP*GP*CP*G)-3')


Mass: 3390.209 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121PECOSY
131TOCSY
141ROESY
151QUIET-NOESY
NMR detailsText: 100MS NOESY, 250MS NOESY 250MS QUIETNOESY 70MS BAND-SELECTIVE J TOCSY FOR PHOSPHOROUS "J SCALE" SET TO 2 AND 3

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Sample preparation

DetailsContents: TRIS
Sample conditionsIonic strength: 50 mM KCL / pH: 7 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY4001
Varian INOVAVarianINOVA5002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
VNMRstructure solution
RefinementMethod: matrix relaxation / Software ordinal: 1
NMR ensembleConformer selection criteria: AVERAGE OF 5 STRUCTURES THAT THE NOESY BACKCALCULATION AGREES WITH EXPERIMENTAL NOESY
Conformers calculated total number: 100 / Conformers submitted total number: 1

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