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Yorodumi- PDB-3qsf: The first crystal structure of a human telomeric G-quadruplex DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qsf | ||||||||||||||||||
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Title | The first crystal structure of a human telomeric G-quadruplex DNA bound to a metal-containing ligand (a nickel complex) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Parallel / telomere / nickel / drug / metal complex | Function / homology | : / Chem-NUF / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | Authors | Campbell, N.H. / Abd Karim, N.H. / Parkinson, G.N. / Vilar, R. / Neidle, S. | Citation | Journal: J.Med.Chem. / Year: 2012 | Title: Molecular basis of structure-activity relationships between salphen metal complexes and human telomeric DNA quadruplexes. Authors: Campbell, N.H. / Karim, N.H. / Parkinson, G.N. / Gunaratnam, M. / Petrucci, V. / Todd, A.K. / Vilar, R. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qsf.cif.gz | 19.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qsf.ent.gz | 12.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qsf_validation.pdf.gz | 617 KB | Display | wwPDB validaton report |
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Full document | 3qsf_full_validation.pdf.gz | 618 KB | Display | |
Data in XML | 3qsf_validation.xml.gz | 3.4 KB | Display | |
Data in CIF | 3qsf_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/3qsf ftp://data.pdbj.org/pub/pdb/validation_reports/qs/3qsf | HTTPS FTP |
-Related structure data
Related structure data | 3qscSC 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans | ||||
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#2: Chemical | #3: Chemical | ChemComp-NUF / [ | #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: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Initial conditions in the 3 ul drop were: 1.25mM quadruplex DNA, 1.25mM ligand, 0.83% PEG (w/v) 10 000, 16.7mM potassium chloride, 16.7mM sodium chloride, 16.7mM lithium sulphate and 20 mM ...Details: Initial conditions in the 3 ul drop were: 1.25mM quadruplex DNA, 1.25mM ligand, 0.83% PEG (w/v) 10 000, 16.7mM potassium chloride, 16.7mM sodium chloride, 16.7mM lithium sulphate and 20 mM potassium cacodylate buffer at pH 7.0. This was equilibrated against a reservoir well solution of 50% (w/v) PEG 10000 , VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 105 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.4866 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4866 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.308→22.01 Å / Num. all: 1888 / Num. obs: 1888 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rsym value: 0.053 / Net I/σ(I): 15.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 36.36 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QSC Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.872 / WRfactor Rfree: 0.3649 / WRfactor Rwork: 0.2714 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.724 / SU B: 9.949 / SU ML: 0.211 / SU R Cruickshank DPI: 0.4976 / SU Rfree: 0.3403 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.34 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.95 Å2 / Biso mean: 34.0311 Å2 / Biso min: 4.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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