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Yorodumi- PDB-5lit: Structure of the DNA duplex d(AAATTT)2 with the potential antipar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lit | ||||||||||||||||||||||||||||
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Title | Structure of the DNA duplex d(AAATTT)2 with the potential antiparasitic drug 6XV at 1.25 A resolution | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / All AT DNA / Antiparasitic Drug / Minor Groove Binding Drug | Function / homology | Chem-6XV / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | Authors | Millan, C.R. / Dardonville, C. / de Koning, H.P. / Saperas, N. / Lourdes Campos, J. | Funding support | Spain, 1items |
Citation | Journal: Nucleic Acids Res. / Year: 2017 | Title: Functional and structural analysis of AT-specific minor groove binders that disrupt DNA-protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast. Authors: Millan, C.R. / Acosta-Reyes, F.J. / Lagartera, L. / Ebiloma, G.U. / Lemgruber, L. / Nue Martinez, J.J. / Saperas, N. / Dardonville, C. / de Koning, H.P. / Campos, J.L. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lit.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lit.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 5lit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/5lit ftp://data.pdbj.org/pub/pdb/validation_reports/li/5lit | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 1807.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.52 % |
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Crystal grow | Temperature: 277.1 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10 mM Magnesium Acetate / PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9787 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.247→36.14 Å / Num. obs: 16801 / % possible obs: 92.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 5.519 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 5.5 / CC1/2: 0.965 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AAATTT Resolution: 1.25→36.14 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.28 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.883 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→36.14 Å
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Refine LS restraints |
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