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Yorodumi- PDB-7z6j: X-ray structure of the adduct obtained upon reaction of [Rh2(OCOC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z6j | ||||||
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Title | X-ray structure of the adduct obtained upon reaction of [Rh2(OCOCH3)(OCOCF3)3] with HEWL | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Protein metalation / dirhodium tetraacetate derivative / dimetallic paddlewheel complexes / model proteins | ||||||
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: 1.53 Å | ||||||
Authors | Loreto, D. / Merlino, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Dalton Trans / Year: 2022 Title: Reactivity of a fluorine-containing dirhodium tetracarboxylate compound with proteins Authors: Loreto, D. / Esposito, A. / Demitri, N. / Guaragna, A. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z6j.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z6j.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 7z6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z6j_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7z6j_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 7z6j_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7z6j_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/7z6j ftp://data.pdbj.org/pub/pdb/validation_reports/z6/7z6j | HTTPS FTP |
-Related structure data
Related structure data | 7z6dC 7z6gC 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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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: P00698, lysozyme | ||||
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#2: Chemical | ChemComp-EPE / | ||||
#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | ChemComp-RH / #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: 2.02 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.10 M HEPES pH 7.5 2.00 M sodium formate |
-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: May 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→39.31 Å / Num. obs: 18041 / % possible obs: 98.8 % / Redundancy: 23.3 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.015 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 25.1 % / Rmerge(I) obs: 1.749 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 899 / CC1/2: 0.752 / Rpim(I) all: 0.5 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.53→39.31 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.297 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.105 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: 27.279 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→39.31 Å
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Refine LS restraints |
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LS refinement shell |
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