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Yorodumi- PDB-6sew: X-ray structure of the gold/lysozyme adduct formed upon 24h expos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sew | ||||||
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Title | X-ray structure of the gold/lysozyme adduct formed upon 24h exposure of protein crystals to compound 2 | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / gold compounds / protein interaction / adduct / soaking / gold binding sites | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Ferraro, G. / Giorgio, A. / Merlino, A. | ||||||
Citation | Journal: Dalton Trans / Year: 2019 Title: Protein-mediated disproportionation of Au(i): insights from the structures of adducts of Au(iii) compounds bearing N,N-pyridylbenzimidazole derivatives with lysozyme. Authors: Ferraro, G. / Giorgio, A. / Mansour, A.M. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sew.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sew.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 6sew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/6sew ftp://data.pdbj.org/pub/pdb/validation_reports/se/6sew | HTTPS FTP |
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-Related structure data
Related structure data | 6setC 6seuC 6sexC 6sezC 193lS S: Starting model for refinement C: citing same article (ref.) |
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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 natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NO3 / #4: Chemical | ChemComp-AU / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% ethylene glycol 0.1 M sodium acetate pH 4.5 0.6 M sodium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→55.39 Å / Num. obs: 6962 / % possible obs: 98.3 % / Redundancy: 5.3 % / CC1/2: 0.752 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.06 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.12→2.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 314 / CC1/2: 0.927 / Rpim(I) all: 0.358 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 2.12→33.99 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.871 / SU B: 7.91 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.271 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 68.15 Å2 / Biso mean: 24.733 Å2 / Biso min: 8.44 Å2
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Refinement step | Cycle: final / Resolution: 2.12→33.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.174 Å / Rfactor Rfree error: 0
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