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Yorodumi- PDB-3qxr: Crystal structure of the brominated CKIT-1 proto-oncogene promote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qxr | ||||||||||||||||||||
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Title | Crystal structure of the brominated CKIT-1 proto-oncogene promoter quadruplex DNA | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DNA quadruplex / regulation / ckit-1 | Function / homology | : / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å | Authors | Wei, D. / Parkinson, G.N. / Neidle, S. | Citation | Journal: Nucleic Acids Res. / Year: 2012 | Title: Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation. Authors: Wei, D. / Parkinson, G.N. / Reszka, A.P. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qxr.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qxr.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 3qxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qxr_validation.pdf.gz | 388.6 KB | Display | wwPDB validaton report |
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Full document | 3qxr_full_validation.pdf.gz | 403.6 KB | Display | |
Data in XML | 3qxr_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 3qxr_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/3qxr ftp://data.pdbj.org/pub/pdb/validation_reports/qx/3qxr | HTTPS FTP |
-Related structure data
Related structure data | 1k8pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 7093.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-K / #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: 1.98 Å3/Da / Density % sol: 37.98 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, potassium chloride, sodium chloride, sodium cacodylate, potassium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→38.55 Å / Num. all: 14007 / Num. obs: 14007 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.62→1.66 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 61.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 1K8P Resolution: 1.62→26.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.172 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE RESIDUAL DENSITY AROUND ATOM OP2 OF RESIDUES A19 AND G20 OF CHAIN B WAS NOT IDENTIFIED.
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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 mean: 20.143 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→26.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.616→1.658 Å / Total num. of bins used: 20
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