+Open data
-Basic information
Entry | Database: PDB / ID: 1ir7 | ||||||
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Title | IM mutant of lysozyme | ||||||
Components | lysozyme | ||||||
Keywords | HYDROLASE / Egg white | ||||||
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: 1.9 Å | ||||||
Authors | Ohmura, T. / Ueda, T. / Hashimoto, Y. / Imoto, T. | ||||||
Citation | Journal: Protein Eng. / Year: 2001 Title: Tolerance of point substitution of methionine for isoleucine in hen egg white lysozyme. Authors: Ohmura, T. / Ueda, T. / Hashimoto, Y. / Imoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ir7.cif.gz | 37 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ir7.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ir7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/1ir7 ftp://data.pdbj.org/pub/pdb/validation_reports/ir/1ir7 | 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: 14349.199 Da / Num. of mol.: 1 / Mutation: I78M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Tissue: egg white / 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: 2.07 Å3/Da / Density % sol: 40.49 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: NaCl, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal grow | *PLUS Method: vapor diffusion |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
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: 1.9→6 Å / Num. obs: 8487 / % possible obs: 84.38 % |
Reflection shell | Resolution: 1.9→1.95 Å / % possible all: 60.7 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. measured all: 37445 / Rmerge(I) obs: 0.0872 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→6 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 6 Å / σ(F): 1 / Rfactor obs: 0.174 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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