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Yorodumi- PDB-8c39: X-ray structure of HEWL upon reaction with a Ruthenium(II)-arene ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c39 | ||||||
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Title | X-ray structure of HEWL upon reaction with a Ruthenium(II)-arene Complexed with Glycosylated Carbene Ligands (5) | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / ruthenium / carbene / protein binding | ||||||
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: 1.2 Å | ||||||
Authors | Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Ruthenium(II)-arene Complexes with Glycosylated Carbene Ligands: Synthesis, Characterization, Antiproliferative Activity, In Solution and Crystallographic Evidences of Macromolecule Binding Authors: Annunziata, A. / Cucciolito, M.E. / Di Ronza, M. / Ferraro, G. / Hadiji, M. / Merlino, A. / Scopelliti, R. / Ruffo, F. / Dyson, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c39.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c39.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8c39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c39_validation.pdf.gz | 794 KB | Display | wwPDB validaton report |
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Full document | 8c39_full_validation.pdf.gz | 795.2 KB | Display | |
Data in XML | 8c39_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 8c39_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/8c39 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/8c39 | HTTPS FTP |
-Related structure data
Related structure data | 8c3bC 193lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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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 AAA
#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 |
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-Non-polymers , 5 types, 190 molecules
#2: Chemical | #3: Chemical | ChemComp-NO3 / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-T8K / [ | #6: Water | ChemComp-HOH / | |
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-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: 1.98 Å3/Da / Density % sol: 37.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% ethylene glycol, 0.1 M sodium acetate buffer at pH 4.0, 0.6 M sodium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→34.63 Å / Num. obs: 37300 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Net I/σ(I): 37.7 |
Reflection shell | Resolution: 1.2→1.21 Å / Redundancy: 15 % / Rmerge(I) obs: 1.789 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1825 / CC1/2: 0.832 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.2→34.63 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.837 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.055 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.694 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→34.63 Å
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Refine LS restraints |
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LS refinement shell |
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