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- PDB-4g0f: Crystal structure of the complex of a human telomeric repeat G-qu... -
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Open data
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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) | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Quadruplex / N-methyl mesoporphyrin IX | Function / homology | : / N-METHYLMESOPORPHYRIN / DNA / DNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() ![]() ![]() Nicoludis, J.M. / Miller, S.T. / Jeffrey, P. / Lawton, T.J. / Rosenzweig, A.C. / Yatsunyk, L.A. | ![]() ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.9 KB | Display | ![]() |
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PDB format | ![]() | 16.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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.) ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-MMP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() | |||||||||
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Phasing MR |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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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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