+Open data
-Basic information
Entry | Database: PDB / ID: 4wo3 | |||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | THE SECOND C-KIT DNA QUADRUPLEX CRYSTAL STRUCTURE | |||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / DNA G-QUADRUPLEX / C/kit | Function / homology | : / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | Authors | Wei, D. / Neidle, S. | Funding support | United Kingdom, 2items |
Citation | Journal: TO BE PUBLISHED | Title: THE SECOND C-KIT1 DNA QUADRUPLEX CRYSTAL STRUCTURE Authors: Wei, D. / Neidle, S. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wo3.cif.gz | 34.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wo3.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wo3_validation.pdf.gz | 381.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4wo3_full_validation.pdf.gz | 381.9 KB | Display | |
Data in XML | 4wo3_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 4wo3_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/4wo3 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/4wo3 | HTTPS FTP |
-Related structure data
Related structure data | 3qxrS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 7028.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.22 % |
---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% MPD, 10 MM MAGNESIUM CHLORIDE, 50 MM POTASSIUM CHLORIDE, AND 50 MM SODIUM CACODYLATE AT PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 105 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Jul 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→28.48 Å / Num. obs: 2439 / % possible obs: 94.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QXR Resolution: 2.73→28.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.901 / SU B: 16.663 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 42.002 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.73→28.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|