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Yorodumi- PDB-5f9x: X-RAY STRUCTURE OF THE ADDUCT BETWEEN HEN EGG WHITE LYSOZYME AND ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f9x | ||||||
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Title | X-RAY STRUCTURE OF THE ADDUCT BETWEEN HEN EGG WHITE LYSOZYME AND CISPLATIN UPON 24 HOURS OF INCUBATION AT 55 DEGREES | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / drug / cisplatin | ||||||
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: 1.94 Å | ||||||
Authors | Russo Krauss, I. / Ferraro, G. / Pica, A. / Merlino, A. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2016 Title: Effect of temperature on the interaction of cisplatin with the model protein hen egg white lysozyme. Authors: Ferraro, G. / Pica, A. / Russo Krauss, I. / Pane, F. / Amoresano, A. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f9x.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f9x.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 5f9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/5f9x ftp://data.pdbj.org/pub/pdb/validation_reports/f9/5f9x | HTTPS FTP |
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-Related structure data
Related structure data | 5f9uC 5fcpC 193lS C: citing same article (ref.) S: Starting model for refinement |
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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 | ChemComp-GOL / | ||
#3: Chemical | #4: 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: 1.96 Å3/Da / Density % sol: 37.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Crystals were grown using a reservoir solution of 1.1 M NaCl, 0.1 M sodium acetate pH 4.4 and a drop of 1 uL adduct solution and 1 uL reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→55.2 Å / Num. obs: 8655 / % possible obs: 98.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.224 / Net I/av σ(I): 5 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.259 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.94→55.15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.535 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.185 / 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: 22.625 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→55.15 Å
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Refine LS restraints |
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