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- PDB-1ycw: Clustered abasic lesions in dna: nmr solution structures of clust... -
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Basic information
Entry | Database: PDB / ID: 1ycw | ||||||
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Title | Clustered abasic lesions in dna: nmr solution structures of clustered bistranded-1 abasic lesion | ||||||
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![]() | DNA / DOUBLE HELIX / ABASIC SITES / CLUSTERED DAMAGE / EXTRUDED RESIDUES / REDUCED AP SITE / FURAN / BISTRANDED ABASIC LESION | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | SOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS | ||||||
![]() | Hazel, R.D. / de los Santos, C. | ||||||
![]() | ![]() Title: NMR solution structures of bistranded abasic site lesions in DNA. Authors: Hazel, R.D. / Tian, K. / de Los Santos, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 69.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 319 KB | Display | ![]() |
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Full document | ![]() | 359.9 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: DNA chain | Mass: 3843.488 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RANDOMLY DESIGNED SEQUENCE CONTAINING STABLE ABASIC SITES (3DR) |
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#2: DNA chain | Mass: 3843.488 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RANDOMLY DESIGNED SEQUENCE CONTAINING STABLE ABASIC SITES (3DR) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
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Sample preparation
Details | Contents: 2mM DUPLEX, 25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA Solvent system: 25 mM PHOSPHATE BUFFER; PH 6.8; 50 mM NaCl; 0.5 mM EDTA. |
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Sample conditions | Ionic strength: NOT DETERMINED / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 Details: 1) HEATING STAGE: FROM 150 TO 500 K IN 70PS. INTRODUCTION OF EXPERIMENTAL RESTRAINTS AT THE END OF THIS STAGE. 2) HIGH TEMPERATURE STAGE: 50 PS DYNAMICS AT 500K 3) COOLING STAGE: FROM 500 TO ...Details: 1) HEATING STAGE: FROM 150 TO 500 K IN 70PS. INTRODUCTION OF EXPERIMENTAL RESTRAINTS AT THE END OF THIS STAGE. 2) HIGH TEMPERATURE STAGE: 50 PS DYNAMICS AT 500K 3) COOLING STAGE: FROM 500 TO 300K IN 40PS. 4) EQUILIBRATION STAGE: 120PS DYNAMICS AT 300K | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 20 / Conformers submitted total number: 5 |