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Yorodumi- PDB-5dwx: Structural Insights into the Quadruplex-Duplex 3' Interface forme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dwx | ||||||
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Title | Structural Insights into the Quadruplex-Duplex 3' Interface formed from a Telomeric Repeat - TLOOP | ||||||
Components |
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Keywords | DNA / Telomere / Quadruplex / Junction / Duplex | ||||||
Function / homology | : / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Parkinson, G.N. / Russo Krauss, I. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Structural Insights into the Quadruplex-Duplex 3' Interface Formed from a Telomeric Repeat: A Potential Molecular Target. Authors: Russo Krauss, I. / Ramaswamy, S. / Neidle, S. / Haider, S. / Parkinson, G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dwx.cif.gz | 25.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dwx.ent.gz | 15.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dwx_validation.pdf.gz | 389.7 KB | Display | wwPDB validaton report |
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Full document | 5dwx_full_validation.pdf.gz | 389.8 KB | Display | |
Data in XML | 5dwx_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 5dwx_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/5dwx ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dwx | HTTPS FTP |
-Related structure data
Related structure data | 5dwwC 1kf1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 7608.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2410.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 61.91 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 2 M lithium sulphate, 50 mM Tris/HCl pH 8.8 2 mM CuCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→42.31 Å / Num. obs: 3820 / % possible obs: 98.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.71→2.78 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.93 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KF1 Resolution: 2.71→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.864 / SU B: 11.596 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.442 / ESU R Free: 0.338 / 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: 52.18 Å2
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Refinement step | Cycle: 1 / Resolution: 2.71→20 Å
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Refine LS restraints |
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