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Yorodumi- PDB-4zee: X-ray structure of the bis-platinum lysozyme adduct formed in the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zee | ||||||
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Title | X-ray structure of the bis-platinum lysozyme adduct formed in the reaction between the protein and the two drugs Cisplatin and Oxaliplatin (preparation 2) | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / ciapltin / oxaliplatin / platin based drugs / cancer | ||||||
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: 1.95 Å | ||||||
Authors | Merlino, A. | ||||||
Citation | Journal: Dalton Trans / Year: 2015 Title: Oxaliplatin vs. cisplatin: competition experiments on their binding to lysozyme. Authors: Marasco, D. / Messori, L. / Marzo, T. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zee.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zee.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/4zee ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zee | HTTPS FTP |
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-Related structure data
Related structure data | 4z46C 4j1aS 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, 149 molecules
#2: Chemical | ChemComp-NO3 / #3: Chemical | #4: Chemical | ChemComp-1PT / | #5: Chemical | ChemComp-CPT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: Best crystals grow within 2-10 days from the following conditions: 0.6 M NaNO3, 0.1 M sodium acetate pH 4.4 and 20 % ethylene glycol. PH range: 4.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: no cryoprotectant |
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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: Jun 27, 2014 |
Radiation | Monochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→54.71 Å / Num. obs: 8452 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.611 / % possible all: 83.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J1A Resolution: 1.95→54.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.418 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.179 / 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: 27.601 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→54.71 Å
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Refine LS restraints |
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