+Open data
-Basic information
Entry | Database: PDB / ID: 4fs6 | ||||||||||||||||||
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Title | Crystal structure of the Z-DNA hexamer CGCGCG at 500 mM CaCl2 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / Ca2+ binding | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | Authors | Chatake, T. / Sunami, T. | Citation | Journal: J.Inorg.Biochem. / Year: 2013 | Title: Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl2 Authors: Chatake, T. / Sunami, T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fs6.cif.gz | 17.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fs6.ent.gz | 11.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fs6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fs6_validation.pdf.gz | 374.5 KB | Display | wwPDB validaton report |
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Full document | 4fs6_full_validation.pdf.gz | 374.5 KB | Display | |
Data in XML | 4fs6_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 4fs6_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/4fs6 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/4fs6 | HTTPS FTP |
-Related 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: 1810.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | #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: 1.94 Å3/Da / Density % sol: 36.66 % |
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Crystal grow | Temperature: 293 K / Method: temperature control / pH: 7 Details: 2.0mM DNA, 20mM Na cacodylate, 30% 2-methyl-2,4-pentanediol, 500mM CaCl2, pH 7.0, TEMPERATURE CONTROL, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2008 |
Radiation | Monochromator: Fixed exit Si (111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.31 |
Reflection | Resolution: 1.3→36 Å / Num. all: 3879 / Num. obs: 3859 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 7.49 Å2 / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 1.3→1.47 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.051 / Num. unique all: 539 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→23.821 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.7962 / σ(F): 2.92 / Phase error: 25.91 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.397 Å2 / ksol: 0.6 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 80.37 Å2 / Biso mean: 12.72 Å2 / Biso min: 1.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→23.821 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3002→13.2757 Å / Total num. of bins used: 1
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