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- PDB-1gdx: CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME SUBSTITUTED AT LEFT-HA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gdx | ||||||
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Title | CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME SUBSTITUTED AT LEFT-HANDED HELICAL POSITIONS | ||||||
![]() | LYSOZYME C | ||||||
![]() | HYDROLASE / Non-glycine Residues at Left-handed Helical Structure / 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 | ![]() ![]() | ||||||
![]() | Takano, K. / Yamagata, Y. / Yutani, K. | ||||||
![]() | ![]() Title: Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme Authors: Takano, K. / Yamagata, Y. / Yutani, K. #1: ![]() Title: Role of Amino Acid Residues at Turns in the Conformational Stability and Folding 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 | ![]() | 42.6 KB | Display | ![]() |
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PDB format | ![]() | 29 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gdwC ![]() 1ge0C ![]() 1ge1C ![]() 1ge2C ![]() 1ge3C ![]() 1ge4C 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: 14634.576 Da / Num. of mol.: 1 / Mutation: R21A 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: 1.92 Å3/Da / Density % sol: 36.02 % | ||||||||||||||||||||||||
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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., (1995) J.Mol.Biol., 254, 62. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 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: 31086 / Num. obs: 10470 / % possible obs: 94.5 % / Rmerge(I) obs: 0.07 |
Reflection | *PLUS Num. measured all: 31086 / Rmerge(I) obs: 0.07 |
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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: ![]() | ||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |