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- PDB-4n9r: X-ray structure of the complex between hen egg white lysozyme and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4n9r | ||||||
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Title | X-ray structure of the complex between hen egg white lysozyme and pentacholrocarbonyliridate(III) (1 day) | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / C-type lysozyme/alpha-lactalbumin family | ||||||
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 | ![]() ![]() | ||||||
![]() | Petruk, A.A. / Bikiel, D.E. / Vergara, A. / Merlino, A. | ||||||
![]() | ![]() Title: Interaction between proteins and Ir based CO releasing molecules: mechanism of adduct formation and CO release. Authors: Petruk, A.A. / Vergara, A. / Marasco, D. / Bikiel, D. / Doctorovich, F. / Estrin, D.A. / 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 | ![]() | 45.5 KB | Display | ![]() |
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PDB format | ![]() | 30.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.6 KB | Display | ![]() |
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Full document | ![]() | 443.9 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nhpC ![]() 4nhqC ![]() 4nhsC ![]() 4nhtC ![]() 4nijC ![]() 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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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) ![]() ![]() | ||||||
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#2: Chemical | ChemComp-2T8 / | ||||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Nonpolymer details | THIS ENTRY REPORTS THE CRYSTAL STRUCTURE OF THE ADDUCT RESULTING FROM THE REACTION OF [IR(CL)5CO]2- ...THIS ENTRY REPORTS THE CRYSTAL STRUCTURE OF THE ADDUCT RESULTING FROM THE REACTION OF [IR(CL)5CO]2- WITH HEN EGG WHITE LYSOZIME (HEWL). THE STARTING METAL COMPLEX EXCHANGE A CL- ION WITH A WATER MOLECULE. THE DATA SUGGEST THAT THE ACTUAL MOLECULE BOUND TO HEWL IS [IRCL4CO(H2O)]-1. THIS EXCHANGE ALSO AGREES WITH PREVIOUS EXPERIMENT | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.95 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.5 Details: Crystals of the complex have been obtained by soaking pre-grown HEWL crystals in a satured solution of Ir(Cl)5CO for 1 day, pH 4.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 34873 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 193L Resolution: 1.55→25.45 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT MODEL USED. 5% DIFFERENCE IN REPORTED AND CALCULATED R-FACTORS
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Refinement step | Cycle: LAST / Resolution: 1.55→25.45 Å
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