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Yorodumi- PDB-6wrm: The interaction of chlorido(1,5-cyclooctadiene)([4-(2-((tert-buto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wrm | ||||||
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Title | The interaction of chlorido(1,5-cyclooctadiene)([4-(2-((tert-butoxycarbonyl)amino)-3-methoxy-3-oxopropyl)-1,3-dimethyl-1H-imidazol-3-ide])rhodium(I) with HEWL after 1 month | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Metal-based / Anticancer / Rhodium / NHC / Carbene / HEWL / Hen egg White Lysozyme / Lysozyme / Metallodrug / Imidazole | ||||||
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: 1.55 Å | ||||||
Authors | Sullivan, M.P. / John, M. / Hartinger, C.G. / Goldstone, D.C. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2020 Title: A Combined Spectroscopic and Protein Crystallography Study Reveals Protein Interactions of Rh I (NHC) Complexes at the Molecular Level. Authors: Daubit, I.M. / Sullivan, M.P. / John, M. / Goldstone, D.C. / Hartinger, C.G. / Metzler-Nolte, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wrm.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wrm.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 6wrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/6wrm ftp://data.pdbj.org/pub/pdb/validation_reports/wr/6wrm | HTTPS FTP |
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-Related structure data
Related structure data | 6wrlC 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
-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: B8YK79, lysozyme |
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-Non-polymers , 5 types, 107 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-RH / | #5: Chemical | ChemComp-U8G / ( | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 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: 1.55→40.51 Å / Num. obs: 17876 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.023 / Rrim(I) all: 0.099 / Net I/σ(I): 19.5 | ||||||||||||||||||||||||||||||
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: 1.55→40.51 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.508 / SU ML: 0.085 / SU R Cruickshank DPI: 0.0986 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.103 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.39 Å2 / Biso mean: 25.533 Å2 / Biso min: 1.68 Å2
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Refinement step | Cycle: final / Resolution: 1.55→40.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0
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