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Yorodumi- PDB-3eum: A bimolecular anti-parallel-stranded Oxytricha nova telomeric qua... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eum | ||||||||||||||||||
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Title | A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6066 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / quadruplex / Oxtyricha nova / BSU-6066 / BSU6066 / anti-parallel / bimolecular / macromolecule / G-quadruplex | Function / homology | : / 3,6-Bis[3-(azepan-1-yl)propionamido]acridine / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 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 | 3eum.cif.gz | 25.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eum.ent.gz | 17.9 KB | Display | PDB format |
PDBx/mmJSON format | 3eum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eum_validation.pdf.gz | 629.9 KB | Display | wwPDB validaton report |
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Full document | 3eum_full_validation.pdf.gz | 631.2 KB | Display | |
Data in XML | 3eum_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 3eum_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/3eum ftp://data.pdbj.org/pub/pdb/validation_reports/eu/3eum | HTTPS FTP |
-Related structure data
Related structure data | 3em2C 3eqwC 3eruC 3es0C 3et8C 3euiC 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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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-NCQ / | #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: 2.09 Å3/Da / Density % sol: 41.23 % | ||||||||||||||||||||||||
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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 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 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: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.540562 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Aug 9, 2007 / Details: Oxford diffraction Nova |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.540562 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→24.35 Å / Num. all: 6576 / Num. obs: 5372 / % possible obs: 81.7 % / Redundancy: 2.3 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.57 |
Reflection shell | Resolution: 1.78→1.93 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.28 / Num. unique all: 539 / % possible all: 39.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1L1H Resolution: 1.78→24.35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 3.508 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.179 / 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: 16.544 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→24.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.83 Å / Total num. of bins used: 20
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