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Open data
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Basic information
Entry | Database: PDB / ID: 1gf4 | ||||||
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Title | BURIED POLAR MUTANT HUMAN LYSOZYME | ||||||
![]() | LYSOZYME | ||||||
![]() | HYDROLASE / buried polar / stability | ||||||
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: Contribution of polar groups in the interior of a protein to the conformational stability. Authors: Takano, K. / Yamagata, Y. / Yutani, K. #1: ![]() Title: Contribution of Salt Bridges near the Surface of a Protein to the Conformational Stability Authors: Takano, K. / Tsuchimori, 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 | ![]() | 43.6 KB | Display | ![]() |
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PDB format | ![]() | 30 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 357.9 KB | Display | ![]() |
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Full document | ![]() | 358.6 KB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gevC ![]() 1gezC ![]() 1gf0C ![]() 1gf3C ![]() 1gf5C ![]() 1gf6C ![]() 1gf7C 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: 14722.666 Da / Num. of mol.: 1 / Mutation: V93T 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: 1.91 Å3/Da / Density % sol: 35.72 % | ||||||||||||||||||||||||
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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: drop contains protein and reservoir solution in a 1:1 ratio | ||||||||||||||||||||||||
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: Sep 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. all: 34979 / Num. obs: 10846 / % possible obs: 98.4 % / Rmerge(I) obs: 0.041 |
Reflection | *PLUS Num. measured all: 34979 |
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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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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refine LS restraints | *PLUS
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