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- PDB-3em2: A bimolecular anti-parallel-stranded Oxytricha nova telomeric qua... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3em2 | ||||||||||||||||||
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Title | A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6038 | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / quadruplex / Oxytricha nova / BSU-6038 / BSU6038 / anti-parallel / bimolecular / macromolecule / G-quadruplex | Function / homology | : / 3,6-Bis[(3-morpholinopropionamido)] acridine / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Campbell, N.H. / Parkinson, G. / Neidle, S. | ![]() ![]() Title: Selectivity in Ligand Recognition of G-Quadruplex Loops. Authors: Campbell, N.H. / Patel, M. / Tofa, A.B. / Ghosh, R. / Parkinson, G.N. / Neidle, S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25.5 KB | Display | ![]() |
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PDB format | ![]() | 17.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 588 KB | Display | ![]() |
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Full document | ![]() | 590.3 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eqwC ![]() 3eruC ![]() 3es0C ![]() 3et8C ![]() 3euiC ![]() 3eumC ![]() 1l1hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The sequence occurs naturally in Oxytricha nova #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-NCE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.86 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2 microliter drops containing 5% v/v MPD, 0.50 mM DNA, 0.25 mM Ligand, 40 mM Potassium chloride, 5 mM Magnesium chloride, 4.1 mM Spermine equilibrated against 35% v/v MPD, pH 7.0, VAPOR ...Details: 2 microliter drops containing 5% v/v MPD, 0.50 mM DNA, 0.25 mM Ligand, 40 mM Potassium chloride, 5 mM Magnesium chloride, 4.1 mM Spermine equilibrated against 35% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 31, 2006 / Details: mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.79 Å / Num. all: 3093 / Num. obs: 3000 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 3.71 % / Biso Wilson estimate: 33.502 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 6.1 / Num. unique all: 303 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1L1H Resolution: 2.3→27.62 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.267 / SU ML: 0.176 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.976 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→27.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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