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- PDB-3gsj: A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gsj | ||||||||||||||||||
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Title | A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / DNA MISMATCH / METALLOINTERCALATOR / DNA RECOGNITION | Function / homology | Chem-R1C / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Zeglis, B.M. / Pierre, V.C. / Kaiser, J.T. / Barton, J.K. | ![]() ![]() Title: A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch: general architecture of the metalloinsertion binding mode Authors: Zeglis, B.M. / Pierre, V.C. / Kaiser, J.T. / Barton, J.K. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.6 KB | Display | ![]() |
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PDB format | ![]() | 15 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 3671.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | ChemComp-CL / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 20 mM sodium cacodylate, 6 mM spermine, 4HCl, 40 mM KCl, 5% MPD, pH 7, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.7 Å / Num. obs: 4469 / % possible obs: 98.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.3 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.081 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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