+Open data
-Basic information
Entry | Database: PDB / ID: 1o0k | ||||||||||||||||||
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Title | Structure of the First Parallel DNA Quadruplex-drug Complex | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / G-4 Quadruplex Drug Complex / Parallel Quadruplex | Function / homology | DAUNOMYCIN / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å | Authors | Clark, G.R. / Pytel, P.D. / Squire, C.J. / Neidle, S. | Citation | Journal: J.Am.Chem.Soc. / Year: 2003 | Title: Structure of the First Parallel DNA Quadruplex-drug Complex Authors: Clark, G.R. / Pytel, P.D. / Squire, C.J. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o0k.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o0k.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 1o0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o0k_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1o0k_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1o0k_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 1o0k_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/1o0k ftp://data.pdbj.org/pub/pdb/validation_reports/o0/1o0k | 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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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 1880.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: TGGGGT synthesized by OSWEL #2: Chemical | #3: Chemical | #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: 2.22 Å3/Da / Density % sol: 44.54 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7 Details: NaCl, Cacodylate buffer, Calcium Chloride, Spermine, MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Type: SSRL / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→99 Å / Num. obs: 20944 / % possible obs: 95.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 32.67 |
Reflection shell | Resolution: 1.17→1.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2031 / % possible all: 87.7 |
Reflection | *PLUS Num. measured all: 202689 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: The first G4 quadruplex from UDF062 Resolution: 1.17→10 Å / Isotropic thermal model: Anisotropic, isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: SHELX
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Refinement step | Cycle: LAST / Resolution: 1.17→10 Å
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.197 / Rfactor Rwork: 0.157 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |