[English] 日本語
Yorodumi- PDB-8ph6: X-ray structure of the adduct formed upon reaction of Lysozyme wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ph6 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the adduct formed upon reaction of Lysozyme with K2[Ru2(DPhF)(CO3)3] in condition B | ||||||
Components | Lysozyme C | ||||||
Keywords | PROTEIN BINDING / Ruthenium / Protein interaction / Metallodrug / Diruthenium / Hydrolase | ||||||
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 | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å | ||||||
Authors | Teran, A. / Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 Title: Steric hindrance and charge influence on the cytotoxic activity and protein binding properties of diruthenium complexes. Authors: Teran, A. / Ferraro, G. / Imbimbo, P. / Sanchez-Pelaez, A.E. / Monti, D.M. / Herrero, S. / Merlino, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ph6.cif.gz | 57 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ph6.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ph6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ph6_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8ph6_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8ph6_validation.xml.gz | 11 KB | Display | |
Data in CIF | 8ph6_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/8ph6 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/8ph6 | HTTPS FTP |
-Related structure data
Related structure data | 8ph5C 8ph7C 8ph8C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-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 |
---|
-Non-polymers , 6 types, 201 molecules
#2: Chemical | ChemComp-EPE / |
---|---|
#3: Chemical | ChemComp-ZWL / [ |
#4: Chemical | ChemComp-YWV / [ |
#5: Chemical | ChemComp-ZWO / |
#6: Chemical | ChemComp-ZXE / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.75 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0 M sodium formate and 0.1 M HEPES buffer at pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→54.36 Å / Num. obs: 51851 / % possible obs: 99.8 % / Redundancy: 19 % / CC1/2: 1 / Rmerge(I) obs: 0.038 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 1.07→1.08 Å / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2477 / CC1/2: 0.833 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→54.36 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.51 / SU ML: 0.026 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.037 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.596 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→54.36 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|