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Yorodumi- PDB-6pla: Adducts formed after 1 month in the reaction of dichlorido(1,3-di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pla | ||||||
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Title | Adducts formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)osmium(II) with HEWL | ||||||
Components | Lysozyme | ||||||
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: 1.25 Å | ||||||
Authors | Sullivan, M.P. / Hartinger, C.G. / Goldstone, D.C. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Probing the Paradigm of Promiscuity for N-Heterocyclic Carbene Complexes and their Protein Adduct Formation. Authors: Sullivan, M.P. / Cziferszky, M. / Tolbatov, I. / Truong, D. / Mercadante, D. / Re, N. / Gust, R. / Goldstone, D.C. / Hartinger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pla.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pla.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 6pla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/6pla ftp://data.pdbj.org/pub/pdb/validation_reports/pl/6pla | HTTPS FTP |
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-Related structure data
Related structure data | 6pl9C 6plbC 4nhiS 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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: B8YK79, lysozyme | ||||||
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#2: Chemical | ChemComp-NA / | ||||||
#3: Chemical | #4: Chemical | ChemComp-OS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.1 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Os(II)(cymene)(1,3-dimethylbenzimidazol-2-ylidene)(Cl)2 (1.04 mg, 1 mg/mL) soak occurred in 0.8 M ...Details: Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Os(II)(cymene)(1,3-dimethylbenzimidazol-2-ylidene)(Cl)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 / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 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: 1.25→37.76 Å / Num. obs: 31598 / % possible obs: 100 % / Redundancy: 26 % / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.029 / Rrim(I) all: 0.149 / Net I/σ(I): 14.5 / Num. measured all: 821371 / Scaling rejects: 122 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NHI Resolution: 1.25→34.21 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.1464 / FOM work R set: 0.8077 / SU B: 2.126 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0463 / SU Rfree: 0.0457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 127.47 Å2 / Biso mean: 18.802 Å2 / Biso min: 11.12 Å2
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Refinement step | Cycle: final / Resolution: 1.25→34.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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