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Yorodumi- PDB-3iju: Chicken egg white lysozyme by highly ordered APA (Anodic Porous A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iju | ||||||
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Title | Chicken egg white lysozyme by highly ordered APA (Anodic Porous Alumina) nanotemplate crystallization method | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / 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: 1.6 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iju.cif.gz | 39.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iju.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 3iju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/3iju ftp://data.pdbj.org/pub/pdb/validation_reports/ij/3iju | HTTPS FTP |
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-Related structure data
Related structure data | 3ijvC 2yvbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.91 % / Mosaicity: 0.42 ° |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9465 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: 0.9465 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→55.907 Å / Num. obs: 16036 / % possible obs: 98.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 21.6 / Num. measured all: 176731 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 2.8 / Num. measured all: 26673 / Num. unique all: 2322 / Rsym value: 0.221 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2yvb Resolution: 1.6→21.57 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.265 / WRfactor Rwork: 0.244 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.845 / SU B: 1.762 / SU ML: 0.065 / SU R Cruickshank DPI: 0.116 / SU Rfree: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 64.53 Å2 / Biso mean: 18.645 Å2 / Biso min: 8.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→21.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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