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Yorodumi- PDB-5ole: X-ray structure of the adduct formed upon reaction of hen egg whi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ole | ||||||
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Title | X-ray structure of the adduct formed upon reaction of hen egg white lysozyme with a tetranuclear Pt-thiosemicarbazone compound | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / ribonuclease / platinum / tetraplatinum / adduct | ||||||
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: 1.78 Å | ||||||
Authors | Ferraro, G. / Merlino, A. | ||||||
Citation | Journal: J. Inorg. Biochem. / Year: 2018 Title: Reactions of a tetranuclear Pt-thiosemicarbazone complex with model proteins. Authors: Marzo, T. / Navas, F. / Cirri, D. / Merlino, A. / Ferraro, G. / Messori, L. / Quiroga, A.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ole.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ole.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 5ole.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/5ole ftp://data.pdbj.org/pub/pdb/validation_reports/ol/5ole | HTTPS FTP |
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-Related structure data
Related structure data | 5oldC 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 , 5 types, 120 molecules
#2: Chemical | #3: Chemical | ChemComp-NO3 / #4: Chemical | #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: 1.97 Å3/Da / Density % sol: 37.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% ethylene glycol 0.1 M sodium acetate pH 4.5 0.6 M sodium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→54.72 Å / Num. obs: 11410 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.1 / Rpim(I) all: 0.959 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.78→54.72 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.535 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.142 / 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: 30.779 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→54.72 Å
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