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Yorodumi- PDB-8ph8: X-ray structure of the adduct formed upon reaction of Lysozyme wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ph8 | ||||||
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Title | X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(DPhF)2(O2CCH3)2] in condition A | ||||||
Components | Lysozyme C | ||||||
Keywords | PROTEIN BINDING / Ruthenium / Protein interaction / Metallodrug / Diruthenium / Hydrolase | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Teran, A. / Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 Title: Steric hindrance and charge influence on the cytotoxic activity and protein binding properties of diruthenium complexes. Authors: Teran, A. / Ferraro, G. / Imbimbo, P. / Sanchez-Pelaez, A.E. / Monti, D.M. / Herrero, S. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ph8.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ph8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ph8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ph8_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ph8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ph8_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 8ph8_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/8ph8 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/8ph8 | HTTPS FTP |
-Related structure data
Related structure data | 8ph5C 8ph6C 8ph7C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | ChemComp-NA / | ||||||
#3: Chemical | ChemComp-SIN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M succinic acid at pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→54.37 Å / Num. obs: 37185 / % possible obs: 99.7 % / Redundancy: 20.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.29→1.31 Å / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1741 / CC1/2: 0.763 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→54.336 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.843 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.054 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: 18.008 Å2
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Refinement step | Cycle: LAST / Resolution: 1.29→54.336 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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