[English] 日本語
Yorodumi- PDB-6bo1: Mono-adduct formed after 3 days in the reaction of dichlorido(1,3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bo1 | ||||||
---|---|---|---|---|---|---|---|
Title | Mono-adduct formed after 3 days in the reaction of dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)ruthenium(II) with HEWL | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / metal-based / anticancer / ruthenium / NHC / carbene / lysozyme / metallodrug / benzimidazole / dimethylbenzimidazole | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.24 Å | ||||||
Authors | Sullivan, M.P. / Hartinger, C.G. / Goldstone, D.C. | ||||||
Citation | Journal: Chem. Commun. (Camb.) / Year: 2018 Title: Unexpected arene ligand exchange results in the oxidation of an organoruthenium anticancer agent: the first X-ray structure of a protein-Ru(carbene) adduct. Authors: Sullivan, M.P. / Nieuwoudt, M.K. / Bowmaker, G.A. / Lam, N.Y.S. / Truong, D. / Goldstone, D.C. / Hartinger, C.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6bo1.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6bo1.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 6bo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/6bo1 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/6bo1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6bo2C 4nhiS S: Starting model for refinement C: citing same article (ref.) |
---|---|
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 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
---|---|
#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-E3D / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | Initially dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)ruthenium(II) was added to ...Initially dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)ruthenium(II) was added to HEWL crystals. The strong electron donating properties of the 1,3-dimethylbenzimidazol-2-ylidene, made the eta6-p-cymene more labile from the Ru centre with an adduct initially formed at His15. To fill the coordination sphere of the Ru, Arg14 and water became coordinated to the Ru centre. The loss of the cymene ligand destabilized the Ru(II) oxidation state resulting in an oxidation to Ru(III). Ultimately forming a dichlorido(1,3-dimethylbenzimidazol-2-ylidene)ruthenium(III) ligand |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.94 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Ru(II)(cymene)(1,3-dimethylbenzimidazol-2-ylidene)(chlorido)2 (1.04 mg, 1 mg/mL) soak occurred in 0. ...Details: Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Ru(II)(cymene)(1,3-dimethylbenzimidazol-2-ylidene)(chlorido)2 (1.04 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.24→55.21 Å / Num. obs: 33258 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.021 / Rrim(I) all: 0.075 / Net I/σ(I): 17.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NHI Resolution: 1.24→55.21 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.174 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0598 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.058 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.44 Å2 / Biso mean: 20.917 Å2 / Biso min: 11.02 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.24→55.21 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.24→1.272 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|