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- PDB-1b60: 3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLE... -

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Basic information

Entry
Database: PDB / ID: 1b60
Title3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS
Components
  • DNA (5'-D(*CP*GP*TP*AP*CP*(EDC)P*CP*AP*TP*GP*C)-3')
  • DNA (5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / ETHENODC / EDC / EXOCYCLIC LESION
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS SIMULATIONS
AuthorsCullinan, D. / Johnson, F. / De Los Santos, C.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Solution structure of an 11-mer duplex containing the 3, N(4)-ethenocytosine adduct opposite 2'-deoxycytidine: implications for the recognition of exocyclic lesions by DNA glycosylases.
Authors: Cullinan, D. / Johnson, F. / de los Santos, C.
#1: Journal: Biochemistry / Year: 1997
Title: Solution Structure of a DNA Duplex Containing the Exocyclic Lesion 3,N4-Etheno- 2'-Deoxycytidine Opposite 2'-Deoxyguanosine
History
DepositionJan 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Atomic model
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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 / _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*TP*AP*CP*(EDC)P*CP*AP*TP*GP*C)-3')
B: DNA (5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,6922
Polymers6,6922
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)1 / 1SEE DETAILS
Representative

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Components

#1: DNA chain DNA (5'-D(*CP*GP*TP*AP*CP*(EDC)P*CP*AP*TP*GP*C)-3') / ETHENODC / EDC / EPSILON-DC


Mass: 3318.184 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3') / ETHENODC / EDC / EPSILON-DC


Mass: 3374.210 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
111NOESY
121COSY
131DQF-COSY
141COSY45
151TOCSY
161HETCORR
NMR detailsText: SEE DETAILS. THE STRUCTURE WAS DETERMINED USING 2D PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED USING THE FULL RELAXATION MATRIX BACK ...Text: SEE DETAILS. THE STRUCTURE WAS DETERMINED USING 2D PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED USING THE FULL RELAXATION MATRIX BACK CALCULATION APPROACH. 15 STRUCTURES EACH WERE DETERMINED FROM A- AND B-FORM DNA BY USING DIFFERENT INITIAL TEMPERATURES AND DIFFERENT LENGTHS OF TIME AT THE HIGH TEMPERATURE STAGE OF THE 30 STRUCTURES FROM DISTANCE RESTRAINED DYNAMICS, 27 HAD AN RMSD TO THEIR AVERAGE OF LESS THAN 0.4 A, SO THE AVERAGE OF THESE 27 WAS USED AS THE STARTING STRUCTURE FOR FULL RELAXATION MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM THIS LAST STEP IS WHAT HAS BEEN DEPOSITED.

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Sample preparation

Sample conditionspH: 6.8 / Temperature: 288 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
X-PLOR3.851BRUNGERrefinement
Felixstructure solution
X-PLORstructure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS SIMULATIONS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: SEE DETAILS / Conformers calculated total number: 1 / Conformers submitted total number: 1

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