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Yorodumi- PDB-1ioq: STABILIZATION OF HEN EGG WHITE LYSOZYME BY A CAVITY-FILLING MUTATION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ioq | ||||||
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Title | STABILIZATION OF HEN EGG WHITE LYSOZYME BY A CAVITY-FILLING MUTATION | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / Glycosidase / Bacteriolytic enzyme | ||||||
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 / Resolution: 1.79 Å | ||||||
Authors | Ohmura, T. / Ueda, T. / Ootsuka, K. / Saito, M. / Imoto, T. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Stabilization of hen egg white lysozyme by a cavity-filling mutation. Authors: Ohmura, T. / Ueda, T. / Ootsuka, K. / Saito, M. / Imoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ioq.cif.gz | 38.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ioq.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ioq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/1ioq ftp://data.pdbj.org/pub/pdb/validation_reports/io/1ioq | HTTPS FTP |
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-Related 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: 14381.154 Da / Num. of mol.: 1 / Mutation: M12F/L56F 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 |
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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: 2.09 Å3/Da / Density % sol: 41.01 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: NaCl, Na-acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal grow | *PLUS |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / 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: 1.79→79.5 Å / Num. all: 10950 / Num. obs: 10634 / % possible obs: 91.07 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.0579 |
Reflection shell | Resolution: 1.78→1.8 Å / Rmerge(I) obs: 0.258 / Num. unique all: 142 / % possible all: 74 |
-Processing
Software |
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Refinement | Resolution: 1.79→6 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.79→6 Å
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Refine LS restraints |
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