- PDB-4zee: X-ray structure of the bis-platinum lysozyme adduct formed in the... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 4zee
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
Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION
-
Sample preparation
Crystal
Density Matthews: 1.96 Å3/Da / Density % sol: 37.36 %
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
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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22986
403
4.8 %
RANDOM
Rwork
0.15877
-
-
-
obs
0.16223
8023
95.85 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK