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- PDB-1di4: ROLE OF AMINO ACID RESIDUES AT TURNS IN THE CONFORMATIONAL STABIL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1di4 | ||||||
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Title | ROLE OF AMINO ACID RESIDUES AT TURNS IN THE CONFORMATIONAL STABILITY AND FOLDING OF HUMAN LYSOZYME | ||||||
![]() | LYSOZYME C | ||||||
![]() | HYDROLASE / STABILITY / TURN / MUTANT | ||||||
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: Role of amino acid residues at turns in the conformational stability and folding of human lysozyme. Authors: Takano, K. / Yamagata, Y. / Yutani, K. #1: ![]() Title: Contribution of Intra-and Intermolecular Hydrogen Bonds to the Conformational Stability of Human Lysozyme Authors: Takano, K. / Yamagata, Y. / Funahashi, J. / Hioki, Y. / Kuramitsu, S. / 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 | ![]() | 37.8 KB | Display | ![]() |
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PDB format | ![]() | 28.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 366.9 KB | Display | ![]() |
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Full document | ![]() | 367.5 KB | Display | |
Data in XML | ![]() | 4 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 14592.563 Da / Num. of mol.: 1 / Mutation: DEL (47-48) 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: 1.81 Å3/Da / Density % sol: 32.02 % | ||||||||||||||||||||||||
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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: 288 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→4 Å / Num. all: 20055 / Num. obs: 7155 / % possible obs: 94.1 % / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.201 / % possible all: 87.8 |
Reflection | *PLUS Num. measured all: 20055 |
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Processing
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Refinement | Resolution: 2→8 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 3 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |