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- PDB-3gsk: 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: 3gsk | ||||||||||||||||||
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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 | CACODYLATE ION / 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 | ![]() | 49.3 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 7.2 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
#1: DNA chain | Mass: 3671.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA #2: Chemical | #3: Chemical | ChemComp-CAC / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.47 % |
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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 NaCl, 5% 2-methyl-2,4-pentanediol, pH 7, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0046 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→35 Å / Num. obs: 22677 / % possible obs: 99.5 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.07 Å2 / ksol: 0.429 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20.271 Å
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LS refinement shell |
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