+Open data
-Basic information
Entry | Database: PDB / ID: 6g5c | ||||||
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Title | Interaction of TiO2 nanoparticles (NM-101) with Lysozyme | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Lysozyme / Titanium dioxide / NM-101 | ||||||
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 / Resolution: 1.8 Å | ||||||
Authors | Sbirkova-Dimitrova, H.I. / Radoslavov, G. / Hristov, P. / Ganev, V. / Dimowa, L. / Rusev, R. / Shivachev, B.L. | ||||||
Funding support | Bulgaria, 1items
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Citation | Journal: Bul.Chem.Commn. / Year: 2018 Title: Crystallization and crystal structure of lysozyme in the presence of nanosized Titanium dioxide Authors: Shivachev, B.L. / Sbirkova-Dimitrova, H.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g5c.cif.gz | 39 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g5c.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 6g5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g5c ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g5c | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Peptide display vector fth1 (others) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 114 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-4TI / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 38.55 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20 mg/ml Lys in TiO2 2.56 mg/ml (JRC NM-101 ) Well/solution 10% (w/v) sodium chloride 0.1 M Sodium acetate buffer pH 5.0 25% (v/v) ethylene glycol drop 4 microliter Lys + 2 microliter TiO2 |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ROTATING ANODE / Type: Agilent SuperNova / Wavelength: 1.8 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→14.5 Å / Num. obs: 10691 / % possible obs: 99.65 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.8→4.8 Å |
-Processing
Software |
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Refinement | Resolution: 1.8→14.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.204 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.121 / 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: 10.369 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→14.5 Å
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Refine LS restraints |
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