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Yorodumi- PDB-4g0f: Crystal structure of the complex of a human telomeric repeat G-qu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g0f | ||||||||||||||||||||
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Title | Crystal structure of the complex of a human telomeric repeat G-quadruplex and N-methyl mesoporphyrin IX (P6) | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Quadruplex / N-methyl mesoporphyrin IX | Function / homology | : / N-METHYLMESOPORPHYRIN / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å | Authors | Nicoludis, J.M. / Miller, S.T. / Jeffrey, P. / Lawton, T.J. / Rosenzweig, A.C. / Yatsunyk, L.A. | Citation | Journal: J.Am.Chem.Soc. / Year: 2012 | Title: Optimized End-Stacking Provides Specificity of N-Methyl Mesoporphyrin IX for Human Telomeric G-Quadruplex DNA. Authors: Nicoludis, J.M. / Miller, S.T. / Jeffrey, P.D. / Barrett, S.P. / Rablen, P.R. / Lawton, T.J. / Yatsunyk, L.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g0f.cif.gz | 23.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g0f.ent.gz | 16.3 KB | Display | PDB format |
PDBx/mmJSON format | 4g0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/4g0f ftp://data.pdbj.org/pub/pdb/validation_reports/g0/4g0f | HTTPS FTP |
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-Related 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: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) | ||||
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#2: Chemical | #3: Chemical | ChemComp-MMP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 50mM lithium cacodylate, 0.625M ammonium acetate, 200mM KCl, 15% PEG400, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2012 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→42.36 Å / Num. all: 5300 / Num. obs: 5300 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.5 / Num. measured all: 6131 / Num. unique all: 782 / % possible all: 98.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→42.36 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.779 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 115.23 Å2 / Biso mean: 53.1948 Å2 / Biso min: 31.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→42.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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