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Yorodumi- PDB-4lgk: X-ray structure of the adduct between hen egg white lysozyme and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lgk | ||||||
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Title | X-ray structure of the adduct between hen egg white lysozyme and Au2Phen, a dinuclear gold(III) complex with -dioxo bridges linking the two metal centers | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / FOURIER SYNTHESIS / Resolution: 1.96 Å | ||||||
Authors | Vergara, A. / Merlino, A. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2013 Title: The mode of action of anticancer gold-based drugs: a structural perspective. Authors: Messori, L. / Scaletti, F. / Massai, L. / Cinellu, M.A. / Gabbiani, C. / Vergara, A. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lgk.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lgk.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 4lgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/4lgk ftp://data.pdbj.org/pub/pdb/validation_reports/lg/4lgk | HTTPS FTP |
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-Related structure data
-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
#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-AU / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THE GOLD COMPOUND FORMING HEWL ADDUCT UNDERGOES EXTENSIVE DEGRADATION UPON REACTION WITH THIS ...THE GOLD COMPOUND FORMING HEWL ADDUCT UNDERGOES EXTENSIVE DEGRADATIO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.76 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
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Detector | Date: Feb 11, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→26.8 Å / Num. all: 7204 / Num. obs: 7204 / % possible obs: 84.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.113 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.96→25.35 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.874 / SU B: 5.65 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→25.35 Å
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