[English] 日本語
Yorodumi- PDB-3ijv: Chicken egg white lysozyme by classical hanging drop vapour diffu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ijv | ||||||
---|---|---|---|---|---|---|---|
Title | Chicken egg white lysozyme by classical hanging drop vapour diffusion method | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Lysozyme / Hen Egg White Lysozyme / Allergen / Antimicrobial / Bacteriolytic enzyme / Disulfide bond / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Pechkova, E. / Tripathi, S.K. / Nicolini, C. | ||||||
Citation | Journal: To be Published Title: Comparison of lysozyme crystals grown by APA and classical hanging drop method Authors: Pechkova, E. / Tripathi, S.K. / Nicolini, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ijv.cif.gz | 39.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ijv.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ijv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/3ijv ftp://data.pdbj.org/pub/pdb/validation_reports/ij/3ijv | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ijuC 2yvbS 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 / Details: Egg / Source: (natural) Gallus gallus (chicken) / Strain: white leghorn / 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: 1.84 Å3/Da / Density % sol: 33.24 % / Mosaicity: 0.35 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 0.04N NaOAc/HOAc buffer, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9787 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 31, 2006 / Details: mirror |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→54.074 Å / Num. obs: 11287 / % possible obs: 93.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 24.3 / Num. measured all: 64864 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 7.8 / Num. measured all: 8536 / Num. unique all: 1500 / Rsym value: 0.075 / % possible all: 87.4 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2yvb Resolution: 1.7→26.26 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.312 / WRfactor Rwork: 0.259 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.841 / SU B: 2.293 / SU ML: 0.079 / SU R Cruickshank DPI: 0.164 / SU Rfree: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 53.74 Å2 / Biso mean: 13.076 Å2 / Biso min: 2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→26.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|