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- PDB-9enz: 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: 9enz | ||||||
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Title | X-ray structure of the adduct formed upon reaction of picoplatin with lysozyme (structure A) | ||||||
![]() | Lysozyme C | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() Lactose synthesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 46.1 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 | ![]() 9eo2C ![]() 9eo5C ![]() 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 115 molecules ![](data/chem/img/NO3.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NH3.gif)
![](data/chem/img/PT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NH3.gif)
![](data/chem/img/PT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.24 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% ethylene glycol, 0.6 M sodium nitrate and 0.1 sodium acetate pH 4.5 |
-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: 1.6→39.203 Å / Num. obs: 15767 / % possible obs: 99.6 % / Redundancy: 21.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 23.5 % / Rmerge(I) obs: 1.2532 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 762 / CC1/2: 0.887 / % possible all: 99.3 |
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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: 26.483 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→39.203 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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