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Yorodumi- PDB-1ht7: STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE LESIO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ht7 | ||||||
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Title | STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE LESION STAGGERED IN A 5'-ORIENTATION. | ||||||
Components |
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Keywords | DNA / double helix / abasic sites / clustered damage / extruded residues. | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / Restrained molecular dynamics | ||||||
Authors | Lin, Z. / de los Santos, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: NMR characterization of clustered bistrand abasic site lesions: effect of orientation on their solution structure. Authors: Lin, Z. / de los Santos, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ht7.cif.gz | 113.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ht7.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ht7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ht7_validation.pdf.gz | 322.7 KB | Display | wwPDB validaton report |
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Full document | 1ht7_full_validation.pdf.gz | 378.7 KB | Display | |
Data in XML | 1ht7_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1ht7_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/1ht7 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/1ht7 | HTTPS FTP |
-Related structure data
-Links
-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: 3867.513 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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-Sample preparation
Details |
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Sample conditions |
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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 / Software ordinal: 1 Details: 1) Heating stage: from 100 to 500 K in 4ps. Introduction of experimental restraints at the end of this stage. 2) High temperature stage: 80 ps dynamics at 500K 3) Cooling stage: From 500 to ...Details: 1) Heating stage: from 100 to 500 K in 4ps. Introduction of experimental restraints at the end of this stage. 2) High temperature stage: 80 ps dynamics at 500K 3) Cooling stage: From 500 to 300K in 40ps. 4) Equilibration stage: 140ps dynamics at 300K. | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 30 / Conformers submitted total number: 6 |