+Open data
-Basic information
Entry | Database: PDB / ID: 4zkk | ||||||||||||||||||||
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Title | The novel double-fold structure of d(GCATGCATGC) | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / folded / minor-groove tetrad / bi-loop / triplet | Function / homology | : / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å | Authors | Thirugnanasambandam, A. / Karthik, S. / Mandal, P.K. / Gautham, N. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 | Title: The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences Authors: Thirugnanasambandam, A. / Karthik, S. / Mandal, P.K. / Gautham, N. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zkk.cif.gz | 22.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zkk.ent.gz | 14.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/4zkk ftp://data.pdbj.org/pub/pdb/validation_reports/zk/4zkk | HTTPS FTP |
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-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: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 51.73 % / Description: hexagonal bipyramidal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 mM DNA, 50 mM sodium cacodylate buffer, 10 mM cobalt chloride and equilibrated against 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.604 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2012 / Details: Bent collimating mirror & toroid |
Radiation | Monochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.604 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 5358 / % possible obs: 98 % / Redundancy: 32 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.8 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.801→24.927 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 0.31 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.801→24.927 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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