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- PDB-9hn6: X-ray structure of the adduct formed upon reaction of the diiodid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9hn6 | ||||||
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Title | X-ray structure of the adduct formed upon reaction of the diiodido analogue of picoplatin with ribonuclease A | ||||||
![]() | Ribonuclease pancreatic | ||||||
![]() | HYDROLASE / platin / interaction / metallodrug / picoplatin / diiodido analogue / ribonuclease | ||||||
Function / homology | ![]() pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferraro, G. / Merlino, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cytotoxicity and Binding to DNA, Lysozyme, Ribonuclease A, and Human Serum Albumin of the Diiodido Analog of Picoplatin. Authors: Ferraro, G. / Pracharova, J. / Gotte, G. / Massai, L. / Berecka, M. / 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 | ![]() | 69.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.2 MB | Display | ![]() |
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Full document | ![]() | 7.2 MB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9hlkC ![]() 9hmkC ![]() 9hmqC ![]() 9hnbC 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
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 167 molecules 








#2: Chemical | ChemComp-NH3 / #3: Chemical | ChemComp-PT / #4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 20% PEG4000, and 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 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→73.45 Å / Num. obs: 23489 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.035 / Rrim(I) all: 0.085 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6936 / CC1/2: 0.86 / Rpim(I) all: 0.393 / Rrim(I) all: 0.966 / % possible all: 100 |
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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: 34.929 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→73.45 Å
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Refine LS restraints |
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LS refinement shell |
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