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Yorodumi- PDB-6g5y: The X-ray structure of the adduct formed in the reaction between ... -
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-Basic information
Entry | Database: PDB / ID: 6g5y | ||||||
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Title | The X-ray structure of the adduct formed in the reaction between lysozyme and a platinum(II) terpyridine compound (acid pH) | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Platinum terpyridine compounds / Protein metalation / ESI MS elucidation / X-Ray structure determination | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Merlino, A. / Ferraro, G. | ||||||
Citation | Journal: Dalton Trans / Year: 2018 Title: A case of extensive protein platination: the reaction of lysozyme with a Pt(ii)-terpyridine complex. Authors: Ferraro, G. / Marzo, T. / Infrasca, T. / Cilibrizzi, A. / Vilar, R. / Messori, L. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g5y.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g5y.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 6g5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g5y ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g5y | 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 | #3: Chemical | ChemComp-PT / #4: Chemical | ChemComp-DMS / #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: 37.68 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 20% ethylene glicol, 0.10 M sodium acetate pH 4.4, 0.60 M sodium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96771 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96771 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→55.51 Å / Num. obs: 18842 / % possible obs: 98.3 % / Redundancy: 3.7 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.025 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.49→1.57 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.672 / Rpim(I) all: 0.219 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→55.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.502 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.097 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.439 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→55.5 Å
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Refine LS restraints |
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