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- PDB-1gfa: CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME SUBSTITUTED AT THE SUR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gfa | ||||||
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Title | CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME SUBSTITUTED AT THE SURFACE POSITIONS | ||||||
![]() | LYSOZYME | ||||||
![]() | HYDROLASE / surface / hydrophilic / stability | ||||||
Function / homology | ![]() antimicrobial humoral response / Antimicrobial peptides / 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 ...antimicrobial humoral response / Antimicrobial peptides / 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 | ![]() ![]() | ||||||
![]() | Funahashi, J. / Takano, K. / Yamagata, Y. / Yutani, K. | ||||||
![]() | ![]() Title: Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability. Authors: Funahashi, J. / Takano, K. / Yamagata, Y. / Yutani, K. #1: ![]() Title: Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme Authors: Funahashi, J. / 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 | ![]() | 43.8 KB | Display | ![]() |
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PDB format | ![]() | 30.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gf8C ![]() 1gf9C ![]() 1gfeC ![]() 1gfgC ![]() 1gfhC ![]() 1gfjC ![]() 1gfkC ![]() 1gfrC ![]() 1gftC ![]() 1gfuC ![]() 1gfvC ![]() 1inuC C: citing same article ( |
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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: 14736.650 Da / Num. of mol.: 1 / Mutation: V2D 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: 35.21 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: sodium phosphate, sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Details: Takano, K., (1985) 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 / Detector: IMAGE PLATE / Date: Feb 6, 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: 31604 / Num. obs: 10329 / % possible obs: 94.3 % / Rmerge(I) obs: 0.05 |
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Processing
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Refinement | Resolution: 1.8→8 Å
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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