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Yorodumi- PDB-8ph7: X-ray structure of the adduct formed upon reaction of Lysozyme wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ph7 | ||||||
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Title | X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(DPhF)(O2CCH3)3] 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: 1.406 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 | 8ph7.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ph7.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ph7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ph7_validation.pdf.gz | 961.8 KB | Display | wwPDB validaton report |
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Full document | 8ph7_full_validation.pdf.gz | 962.4 KB | Display | |
Data in XML | 8ph7_validation.xml.gz | 9 KB | Display | |
Data in CIF | 8ph7_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/8ph7 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/8ph7 | HTTPS FTP |
-Related structure data
Related structure data | 8ph5C 8ph6C 8ph8C 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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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 A
#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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-Non-polymers , 5 types, 110 molecules
#2: Chemical | ChemComp-ZQ2 / [ |
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#3: Chemical | ChemComp-SIN / |
#4: Chemical | ChemComp-ZWH / [ |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-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: 1.406→54.921 Å / Num. obs: 14799 / % possible obs: 99.4 % / Redundancy: 19.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.164 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.406→1.53 Å / Rmerge(I) obs: 2.764 / Mean I/σ(I) obs: 2 / Num. unique obs: 742 / CC1/2: 0.867 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.406→54.921 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.317 / SU ML: 0.087 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.131 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: 24.732 Å2
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Refinement step | Cycle: LAST / Resolution: 1.406→54.921 Å
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Refine LS restraints |
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LS refinement shell |
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