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Yorodumi- PDB-1b60: 3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b60 | ||||||
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Title | 3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS | ||||||
Components |
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Keywords | DNA / ETHENODC / EDC / EXOCYCLIC LESION | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS SIMULATIONS | ||||||
Authors | Cullinan, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b60.cif.gz | 24.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b60.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/1b60 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/1b60 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3318.184 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | 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 ...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. |
-Sample preparation
Sample conditions | pH: 6.8 / Temperature: 288 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: RESTRAINED MOLECULAR DYNAMICS SIMULATIONS / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: SEE DETAILS / Conformers calculated total number: 1 / Conformers submitted total number: 1 |