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Yorodumi- PDB-7beb: Unusual structural features in the adduct of dirhodium tetraaceta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7beb | ||||||
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Title | Unusual structural features in the adduct of dirhodium tetraacetate with lysozyme (4) | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Metal/protein adduct / dimetallic complex / metallodrug | ||||||
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: 1.32 Å | ||||||
Authors | Loreto, D. / Ferraro, G. / Merlino, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Int J Mol Sci / Year: 2021 Title: Unusual Structural Features in the Adduct of Dirhodium Tetraacetate with Lysozyme. Authors: Loreto, D. / Ferraro, G. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7beb.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7beb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7beb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7beb_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7beb_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7beb_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 7beb_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/7beb ftp://data.pdbj.org/pub/pdb/validation_reports/be/7beb | HTTPS FTP |
-Related structure data
Related structure data | 7bdzC 7be0C 7be1C 7be2C 7becC 193lS 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 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, lysozyme |
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-Non-polymers , 6 types, 147 molecules
#2: Chemical | #3: Chemical | ChemComp-NO3 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACT / #7: 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: 2.01 Å3/Da / Density % sol: 38.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium acetate, 20% ethylene glicol, 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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→55.58 Å / Num. obs: 26513 / % possible obs: 95.4 % / Redundancy: 25.8 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.013 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.32→1.37 Å / Redundancy: 25.9 % / Rmerge(I) obs: 2.55 / Num. unique obs: 1327 / CC1/2: 0.612 / Rpim(I) all: 0.72 / % possible all: 51.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193l Resolution: 1.32→55.58 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.223 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.069 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: 27.339 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→55.58 Å
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Refine LS restraints |
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LS refinement shell |
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