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Yorodumi- PDB-3eru: A bimolecular anti-parallel-stranded Oxytricha nova telomeric qua... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eru | ||||||||||||||||||
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Title | A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6045 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / quadruplex / Oxytricha nova / BSU-6045 / BSU6045 / anti-parallel / bimolecular / macromolecule / G-quadruplex / telomere | Function / homology | : / Chem-NCJ / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | Authors | Campbell, N.H. / Parkinson, G. / Neidle, S. | Citation | Journal: Biochemistry / Year: 2009 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eru.cif.gz | 26.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eru.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 3eru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eru_validation.pdf.gz | 591 KB | Display | wwPDB validaton report |
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Full document | 3eru_full_validation.pdf.gz | 592.1 KB | Display | |
Data in XML | 3eru_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 3eru_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/3eru ftp://data.pdbj.org/pub/pdb/validation_reports/er/3eru | HTTPS FTP |
-Related structure data
Related structure data | 3em2C 3eqwC 3es0C 3et8C 3euiC 3eumC 1l1hS S: Starting model for refinement C: citing same article (ref.) |
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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
#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-NCJ / | #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: 2.08 Å3/Da / Density % sol: 40.77 % | ||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 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→23.18 Å / Num. all: 4619 / Num. obs: 4422 / % possible obs: 95.7 % / Observed criterion σ(I): 3 / Redundancy: 3.77 % / Biso Wilson estimate: 27.559 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.72 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 6.4 / Num. unique all: 458 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1L1H Resolution: 2→22.72 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU ML: 0.124 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.197 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.439 Å2
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Refinement step | Cycle: LAST / Resolution: 2→22.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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