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Yorodumi- PDB-8boy: X-ray structure of the adduct formed upon reaction of the five-co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8boy | ||||||
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Title | X-ray structure of the adduct formed upon reaction of the five-coordinate Pt(II) complex, 1-Me,Me, with HEWL at pH 4.0 | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / platinum / five-coordinate / glucoconjugate / metallodrug / protein interaction | ||||||
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: 1.33 Å | ||||||
Authors | Ferraro, G. / Tito, G. / Merlino, A. | ||||||
Funding support | 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Impact of Hydrophobic Chains in Five-Coordinate Glucoconjugate Pt(II) Anticancer Agents. Authors: Annunziata, A. / Imbimbo, P. / Cucciolito, M.E. / Ferraro, G. / Langellotti, V. / Marano, A. / Melchiorre, M. / Tito, G. / Trifuoggi, M. / Monti, D.M. / Merlino, A. / Ruffo, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8boy.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8boy.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8boy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8boy_validation.pdf.gz | 769.7 KB | Display | wwPDB validaton report |
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Full document | 8boy_full_validation.pdf.gz | 770.2 KB | Display | |
Data in XML | 8boy_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 8boy_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/8boy ftp://data.pdbj.org/pub/pdb/validation_reports/bo/8boy | HTTPS FTP |
-Related structure data
Related structure data | 8bovC 193lS S: Starting model for refinement 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-NO3 / #3: Chemical | ChemComp-R0I / | #4: Chemical | ChemComp-PT / | #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: 1.97 Å3/Da / Density % sol: 37.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% ethylene glycol 0.1 M sodium acetate pH 4.0 0.6 M sodium Nitrate |
-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: 1.33→54.801 Å / Num. obs: 27087 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.038 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.251 / Mean I/σ(I) obs: 2 / Num. unique obs: 1342 / CC1/2: 0.812 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.33→54.801 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.173 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 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: 23.908 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→54.801 Å
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Refine LS restraints |
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LS refinement shell |
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