[English] 日本語
Yorodumi- PDB-1flu: HEN EGG WHITE LYSOZYME MUTANT WITH ALANINE SUBSTITUTED FOR GLYCINE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1flu | ||||||
---|---|---|---|---|---|---|---|
Title | HEN EGG WHITE LYSOZYME MUTANT WITH ALANINE SUBSTITUTED FOR GLYCINE | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / HEN LYSOZYME / ALANINE SCANNING | ||||||
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 / Resolution: 1.785 Å | ||||||
Authors | Masumoto, K. / Ueda, T. / Motoshima, H. / Imoto, T. | ||||||
Citation | Journal: Protein Eng. / Year: 2000 Title: Relationship between local structure and stability in hen egg white lysozyme mutant with alanine substituted for glycine Authors: Masumoto, K. / Ueda, T. / Motoshima, H. / Imoto, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1flu.cif.gz | 33.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1flu.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 1flu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1flu_validation.pdf.gz | 354.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1flu_full_validation.pdf.gz | 354.2 KB | Display | |
Data in XML | 1flu_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1flu_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/1flu ftp://data.pdbj.org/pub/pdb/validation_reports/fl/1flu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14345.186 Da / Num. of mol.: 1 / Mutation: G67A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PAM82 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00698, lysozyme |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: sodium chloride, sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 3.2 / PH range high: 2.4 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.785→6 Å / Num. all: 12048 / Num. obs: 10452 / Redundancy: 1.15 % / Rmerge(I) obs: 0.0558 |
Reflection | *PLUS % possible obs: 86.8 % / Num. measured all: 12048 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.785→6 Å / Cross valid method: THROUGHOUT
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.785→6 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.25 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |