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Yorodumi- PDB-3ey0: A new form of DNA-drug interaction in the minor groove of a coile... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ey0 | ||||||||||||||||||
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Title | A new form of DNA-drug interaction in the minor groove of a coiled coil | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DNA drug pentamidine coiled-coil all-AT | Function / homology | 1,5-BIS(4-AMIDINOPHENOXY)PENTANE / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | Authors | Pous, J. / Moreno, T. / Subirana, J.A. / Campos, J.L. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 | Title: Coiled-coil conformation of a pentamidine-DNA complex Authors: Moreno, T. / Pous, J. / Subirana, J.A. / 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 | 3ey0.cif.gz | 22.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ey0.ent.gz | 15.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ey0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ey0_validation.pdf.gz | 561.5 KB | Display | wwPDB validaton report |
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Full document | 3ey0_full_validation.pdf.gz | 561.5 KB | Display | |
Data in XML | 3ey0_validation.xml.gz | 3.4 KB | Display | |
Data in CIF | 3ey0_validation.cif.gz | 4.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3ey0 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3ey0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Double stranded ATATATATAT |
-Components
#1: DNA chain | Mass: 3042.041 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized by using phosphoramiditine method #2: Chemical | ChemComp-PNT / | #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: 2.86 Å3/Da / Density % sol: 56.95 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20 mM MgCl2, 50 mM MES, 15% Isopropanol, 3.62 mM ds-DNA, 16.86 mM PNT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278.15K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 104 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2008 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→50 Å / Num. all: 2899 / Num. obs: 2899 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 15.8 % / Biso Wilson estimate: 56.01 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 37.625 |
Reflection shell | Resolution: 2.52→2.56 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 15.75 / Num. unique all: 128 / Rsym value: 0.212 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: standard watson-crick DNA Resolution: 2.52→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.885 / SU B: 25.145 / SU ML: 0.238 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.52 / ESU R Free: 0.323 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.499 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.59 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.2235 Å / Origin y: 10.8519 Å / Origin z: 90.3531 Å
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