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Yorodumi- PDB-8bov: X-ray structure of the adduct formed upon reaction of the five-co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bov | ||||||
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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 7.5 | ||||||
Components | Lysozyme | ||||||
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: 1.25 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 | 8bov.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bov.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8bov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bov_validation.pdf.gz | 883.4 KB | Display | wwPDB validaton report |
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Full document | 8bov_full_validation.pdf.gz | 887.7 KB | Display | |
Data in XML | 8bov_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 8bov_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/8bov ftp://data.pdbj.org/pub/pdb/validation_reports/bo/8bov | HTTPS FTP |
-Related structure data
Related structure data | 8boyC 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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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) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 145 molecules
#2: Chemical | ChemComp-EPE / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-R0I / | #5: Chemical | ChemComp-DMS / | #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 Å3/Da / Density % sol: 38.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 M sodium formate 0.1 M Hepes buffer pH 7.5 |
-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: 1.25→55.564 Å / Num. obs: 32632 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 12 % / Rmerge(I) obs: 1.069 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1623 / CC1/2: 0.854 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.25→55.564 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.874 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.056 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: 19.592 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→55.564 Å
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Refine LS restraints |
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LS refinement shell |
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