[English] 日本語
Yorodumi- PDB-2i6z: X-ray diffraction studies of adducts between anticancer platinum ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i6z | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray diffraction studies of adducts between anticancer platinum drugs and hen egg white lysozyme | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / cisplatin-lysozyme adduct / anticancer drugs | ||||||
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 | Temperini, C. / Casini, A. / Messori, L. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2007 Title: ESI mass spectrometry and X-ray diffraction studies of adducts between anticancer platinum drugs and hen egg white lysozyme. Authors: Casini, A. / Mastrobuoni, G. / Temperini, C. / Gabbiani, C. / Francese, S. / Moneti, G. / Supuran, C.T. / Scozzafava, A. / Messori, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2i6z.cif.gz | 41.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2i6z.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 2i6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/2i6z ftp://data.pdbj.org/pub/pdb/validation_reports/i6/2i6z | HTTPS FTP |
---|
-Related structure data
Related structure data | 193lS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: Residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
---|---|
#2: Chemical | ChemComp-CPT / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-DMS / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.05 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5 mM sodium acetate buffer, pH 6.5 and 0.05 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å |
Detector | Type: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Jul 11, 2006 |
Radiation | Monochromator: capillary / 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→20 Å / Num. all: 11008 / Num. obs: 9290 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 91.3 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 193L Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: maximum likelihood
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
| ||||||||||||||||
Refine LS restraints |
| ||||||||||||||||
LS refinement shell | Resolution: 1.9→2 Å /
|