+Open data
-Basic information
Entry | Database: PDB / ID: 4fs5 | ||||||||||||||||||
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Title | Crystal structure of the Z-DNA hexamer CGCGCG at 500 mM MgCl2 | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / Mg2+ 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 | 4fs5.cif.gz | 26.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fs5.ent.gz | 17.9 KB | Display | PDB format |
PDBx/mmJSON format | 4fs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fs5_validation.pdf.gz | 383.9 KB | Display | wwPDB validaton report |
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Full document | 4fs5_full_validation.pdf.gz | 384 KB | Display | |
Data in XML | 4fs5_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 4fs5_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/4fs5 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/4fs5 | HTTPS FTP |
-Related structure data
Related structure data | 4fs6C 1io5S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #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 Å3/Da / Density % sol: 38.62 % |
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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-pentainediol, 500mM MgCl2, 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 | Resolution: 1.3→24.2 Å / Num. all: 6915 / Num. obs: 6868 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.12 / Num. unique all: 1006 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IO5 Resolution: 1.3→9.682 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7407 / SU ML: 0.2 / σ(F): 0.16 / Phase error: 32.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.456 Å2 / ksol: 0.6 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 30.13 Å2 / Biso mean: 14.8432 Å2 / Biso min: 7.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→9.682 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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