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- PDB-7bdz: X-ray structure of Hen Egg White Lysozyme with dirhodium tetraace... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bdz | ||||||
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Title | X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (1) | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / Metallodrug / Metal/protein adduct / bimetallic compounds | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Loreto, D. / Merlino, A. / Ferraro, G. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7be0C ![]() 7be1C ![]() 7be2C ![]() 7bebC ![]() 7becC ![]() 193lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() ![]() |
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-Non-polymers , 5 types, 147 molecules ![](data/chem/img/NO3.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/RH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/RH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NO3 / #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Chemical | ChemComp-RH / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M 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: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→25.48 Å / Num. obs: 8895 / % possible obs: 99 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.045 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.94→1.97 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 426 / CC1/2: 0.808 / Rpim(I) all: 0.249 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 193l Resolution: 1.94→25.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.66 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.164 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: 21.212 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→25.48 Å
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Refine LS restraints |
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LS refinement shell |
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