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Yorodumi- PDB-5ihd: Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ihd | |||||||||||||||||||||||||||||||
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Title | Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), complexed by L-lactate and succinate | |||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / copper(II) | Function / homology | (2S)-2-HYDROXYPROPANOIC ACID / COPPER (II) ION / SUCCINIC ACID / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | Authors | Rohner, M. / Medina-Molner, A. / Spingler, B. | Funding support | Switzerland, 1items |
Citation | Journal: Inorg.Chem. / Year: 2016 | Title: N,N,O and N,O,N Meridional cis Coordination of Two Guanines to Copper(II) by d(CGCGCG)2. Authors: Rohner, M. / Medina-Molner, A. / Spingler, B. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ihd.cif.gz | 29.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ihd.ent.gz | 18.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ihd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/5ihd ftp://data.pdbj.org/pub/pdb/validation_reports/ih/5ihd | HTTPS FTP |
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-Related structure data
Related structure data | 4xqzC 4xsnC 2dcgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-DNA chain , 1 types, 4 molecules ABCD
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 142 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SIN / | #6: 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: 38.48 % |
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Crystal grow | Temperature: 296 K / Method: microbatch / pH: 6 Details: 1.2 mM d(CG)3, 1.2 mM di copper complex, 0.25 M MES pH 6, 25 mM Ca(lactate)2, 2.5% EtOAc |
-Data collection
Diffraction | Mean temperature: 183 K |
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Diffraction source | Source: SEALED TUBE / Type: Long fine focus / Wavelength: 1.54 Å |
Detector | Type: STOE / Detector: IMAGE PLATE / Date: Nov 7, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→26.215 Å / Num. obs: 7934 / % possible obs: 97.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.51 |
Reflection shell | Resolution: 1.57→1.7 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.1736 / Mean I/σ(I) obs: 3.77 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DCG Resolution: 1.57→26.215 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→26.215 Å
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Refine LS restraints |
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LS refinement shell |
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