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Yorodumi- PDB-4oot: X-ray structure of the protein-gold adduct formed upon reaction o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oot | ||||||
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Title | X-ray structure of the protein-gold adduct formed upon reaction of Aubipic with hen egg white lysozyme | ||||||
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: 1.8 Å | ||||||
Authors | Merlino, A. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2014 Title: Protein Recognition of Gold-Based Drugs: 3D Structure of the Complex Formed When Lysozyme Reacts with Aubipy(c.). Authors: Messori, L. / Cinellu, M.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 | 4oot.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oot.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 4oot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/4oot ftp://data.pdbj.org/pub/pdb/validation_reports/oo/4oot | HTTPS FTP |
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-Related structure data
Related structure data | 4j1aS S: Starting model for refinement |
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Similar 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 genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Description: purchased from SIGMA / Gene: LYZ / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | ChemComp-AU / | ||||
#3: Chemical | #4: Chemical | ChemComp-NO3 / #5: Water | ChemComp-HOH / | |
-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: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: crystal of lysozyme have been obtained in the presence of Aubipyc (1:10 protein to metal ratio) via the hanging drop vapor diffusion method. These crystals have been grown using a reservoir ...Details: crystal of lysozyme have been obtained in the presence of Aubipyc (1:10 protein to metal ratio) via the hanging drop vapor diffusion method. These crystals have been grown using a reservoir solution of 0.6 M NaNO3, 0.1 M sodium acetate pH 4.4 and 20 % ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD |
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: 1.8→50 Å / Num. all: 10554 / Num. obs: 10554 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.048 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB code 4J1A Resolution: 1.8→25.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.933 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.16 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25.55 Å
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Refine LS restraints |
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