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- PDB-9eo5: X-ray structure of the adduct formed upon reaction of picoplatin ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9eo5 | ||||||
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Title | X-ray structure of the adduct formed upon reaction of picoplatin with bovine pancreatic ribonuclease (structure C) | ||||||
![]() | Ribonuclease pancreatic![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Picoplatin binding to proteins: X-ray structures and mass spectrometry data on the adducts with lysozyme and ribonuclease A. Authors: Ferraro, G. / Lyckova, T. / Massai, L. / Starha, P. / Messori, L. / Merlino, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9enzC ![]() 9eo2C ![]() 9eo8C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NH3 / ![]() #3: Chemical | ChemComp-PT / #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.31 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 22% PEG4000, 0.1 M sodium citrate pH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.99→50.424 Å / Num. obs: 16745 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.161 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.99→2.08 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 844 / CC1/2: 0.638 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.756 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→50.424 Å
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Refine LS restraints |
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LS refinement shell |
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