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Open data
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Basic information
Entry | Database: PDB / ID: 1ix0 | ||||||
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Title | I59A-3SS human lysozyme | ||||||
![]() | lysozyme | ||||||
![]() | HYDROLASE / stability / water | ||||||
Function / homology | ![]() antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Takano, K. / Yamagata, Y. / Yutani, K. | ||||||
![]() | ![]() Title: Buried water molecules contribute to the conformational stability of a protein Authors: Takano, K. / Yamagata, Y. / Yutani, K. #1: ![]() Title: A general rule for the relationship between hydrophobic effect and conformational stability of a protein: stability and structure of a series of hydrophobic mutants of human lysozyme Authors: Takano, K. / Yamagata, Y. / Yutani, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.2 KB | Display | ![]() |
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PDB format | ![]() | 29.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 364.1 KB | Display | ![]() |
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Full document | ![]() | 365 KB | Display | |
Data in XML | ![]() | 3.9 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14614.482 Da / Num. of mol.: 1 / Mutation: I59A/C77A/C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.25 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: NaCl, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusion, hanging drop / Details: Takano, K., (1995) J.Mol.Biol., 254, 62. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 27, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. all: 50796 / Num. obs: 10772 / % possible obs: 99 % |
Reflection | *PLUS Num. measured all: 50796 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 98.5 % / Rmerge(I) obs: 0.056 / Mean I/σ(I) obs: 35 |
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Processing
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Refinement | Method to determine structure: isomorphous / Resolution: 1.8→8 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refinement | *PLUS Rfactor Rfree: 0.256 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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