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Yorodumi- PDB-1oua: CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE STABILITY OF HUMAN LY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oua | ||||||
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Title | CONTRIBUTION OF HYDROPHOBIC RESIDUES TO THE STABILITY OF HUMAN LYSOZYME: X-RAY STRUCTURE OF THE I56T MUTANT | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE (O-GLYCOSYL) / AMYLOID / DISEASE MUTATION | ||||||
Function / homology | Function and homology information antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.8 Å | ||||||
Authors | Takano, K. / Funahashi, J. / Yamagata, Y. / Ogasahara, K. / Yutani, K. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 1996 Title: The structure, stability, and folding process of amyloidogenic mutant human lysozyme. Authors: Funahashi, J. / Takano, K. / Ogasahara, K. / Yamagata, Y. / Yutani, K. #1: Journal: J.Mol.Biol. / Year: 1995 Title: Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants Authors: Takano, K. / Ogasahara, K. / Kaneda, H. / Yamagata, Y. / Fujii, S. / Kanaya, E. / Kikuchi, M. / Oobatake, M. / Yutani, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oua.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oua.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/1oua ftp://data.pdbj.org/pub/pdb/validation_reports/ou/1oua | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14708.639 Da / Num. of mol.: 1 / Mutation: I56T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN LYSOZYME WITH ILE 56 REP / Plasmid: PERI8602 Gene (production host): HUMAN LYSOZYME WITH ILE 56 REPLACED BY THR Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AH22R- / References: UniProt: P61626, lysozyme |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.09 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 23, 1996 |
Radiation | 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. obs: 9220 / % possible obs: 80.4 % / Observed criterion σ(I): 1 / Redundancy: 3.05 % / Rmerge(I) obs: 0.056 |
Reflection | *PLUS Num. measured all: 28187 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / 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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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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