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Yorodumi- PDB-2lo5: Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Reco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lo5 | ||||||||||||||||||||
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Title | Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA, Structure of a Thymine bulge | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / thymine bulge / hairpin / Bifunctional Zn(II) Macrocyclic Complex | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | Model details | fewest violations, model 1 | Authors | Morrow, J.R. / Fountain, M.A. / del Mundo, I.A. / Siter, K.E. | Citation | Journal: Inorg.Chem. / Year: 2012 | Title: Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA. Authors: Del Mundo, I.M. / Siters, K.E. / Fountain, M.A. / Morrow, J.R. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lo5.cif.gz | 161.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lo5.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 2lo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lo5_validation.pdf.gz | 412.4 KB | Display | wwPDB validaton report |
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Full document | 2lo5_full_validation.pdf.gz | 635.5 KB | Display | |
Data in XML | 2lo5_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 2lo5_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/2lo5 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/2lo5 | 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: 3664.380 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: NMR structure of a d(GGCCGCAGTGCC)sequence | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 6 / NA beta-angle constraints total count: 7 / NA chi-angle constraints total count: 6 / NA delta-angle constraints total count: 11 / NA epsilon-angle constraints total count: 6 / NA gamma-angle constraints total count: 0 / NA sugar pucker constraints total count: 0 / NOE constraints total: 118 / NOE long range total count: 64 | ||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 2.76 ° Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 1000 / Conformers submitted total number: 18 / Maximum lower distance constraint violation: 0.39 Å / Maximum torsion angle constraint violation: 4.1 ° / Maximum upper distance constraint violation: 0.25 Å | ||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0266 Å / Distance rms dev error: 0.0018 Å |