[English] 日本語
Yorodumi- PDB-3a94: Crystal structure of hen egg white lysozyme soaked with 100mM RhCl3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a94 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of hen egg white lysozyme soaked with 100mM RhCl3 | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Allergen / Antimicrobial / Bacteriolytic enzyme / Glycosidase | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Abe, S. / Koshiyama, T. / Ohki, T. / Hikage, T. / Watanabe, Y. / Ueno, T. | ||||||
Citation | Journal: Chemistry / Year: 2010 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 |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3a94.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3a94.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 3a94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/3a94 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/3a94 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3a8zC 3a90C 3a91C 3a92C 3a93C 3a95C 3a96C 193lS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-RH3 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.93 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 27, 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: 1.55→80 Å / Num. obs: 17274 / % possible obs: 99.8 % / Redundancy: 23.1 % / Biso Wilson estimate: 18.832 Å2 / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 23.2 % / Rmerge(I) obs: 0.26 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 193L Resolution: 1.55→16.49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.437 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.117 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→16.49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
|