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- PDB-3a96: Crystal structure of hen egg white lysozyme soaked with 100mM RhC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a96 | ||||||
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Title | Crystal structure of hen egg white lysozyme soaked with 100mM RhCl3 at pH2.2 | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / Allergen / Antimicrobial / Bacteriolytic enzyme / Disulfide bond / Glycosidase | ||||||
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 | ![]() ![]() | ||||||
![]() | Abe, S. / Koshiyama, T. / Ohki, T. / Hikage, T. / Watanabe, Y. / Ueno, T. | ||||||
![]() | ![]() Title: Elucidation of Metal-Ion Accumulation Induced by Hydrogen Bonds on Protein Surfaces by Using Porous Lysozyme Crystals Containing Rh(III) Ions as the Model Surfaces Authors: Ueno, T. / Abe, S. / Koshiyama, T. / Ohki, T. / Hikage, T. / Watanabe, Y. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.5 KB | Display | ![]() |
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PDB format | ![]() | 28.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.3 KB | Display | ![]() |
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Full document | ![]() | 426 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a8zC ![]() 3a90C ![]() 3a91C ![]() 3a92C ![]() 3a93C ![]() 3a94C ![]() 3a95C ![]() 193lS C: citing same article ( S: Starting model for refinement |
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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-NA / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-RH3 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 2, 2008 |
Radiation | Monochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→80 Å / Num. obs: 11665 / % possible obs: 96.1 % / Redundancy: 21.5 % / Biso Wilson estimate: 22.778 Å2 / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 21.5 % / Rmerge(I) obs: 0.325 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 193L Resolution: 1.75→18.38 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.31 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→18.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.747→1.792 Å / Total num. of bins used: 20
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