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Yorodumi- PDB-6set: X-ray structure of the gold/lysozyme adduct formed upon 3 days ex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6set | ||||||
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Title | X-ray structure of the gold/lysozyme adduct formed upon 3 days exposure of protein crystals to compound 1 | ||||||
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: 1.9 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 | 6set.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6set.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 6set.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/6set ftp://data.pdbj.org/pub/pdb/validation_reports/se/6set | HTTPS FTP |
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-Related structure data
Related structure data | 6seuC 6sewC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 7 types, 155 molecules
#2: Chemical | ChemComp-NO3 / #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 1.95 Å3/Da / Density % sol: 37 % |
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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: Mar 6, 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: 1.9→30.86 Å / Num. obs: 8972 / % possible obs: 95 % / Redundancy: 7.7 % / CC1/2: 0.648 / Rmerge(I) obs: 0.0107 / Rpim(I) all: 0.044 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 399 / CC1/2: 0.887 / Rpim(I) all: 0.36 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.9→30.86 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.873 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.16 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: 87.75 Å2 / Biso mean: 28.257 Å2 / Biso min: 11.31 Å2
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Refinement step | Cycle: final / Resolution: 1.9→30.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.948 Å / Rfactor Rfree error: 0
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