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Yorodumi- PDB-1lz4: ENTHALPIC DESTABILIZATION OF A MUTANT HUMAN LYSOZYME LACKING A DI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lz4 | ||||||
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Title | ENTHALPIC DESTABILIZATION OF A MUTANT HUMAN LYSOZYME LACKING A DISULFIDE BRIDGE BETWEEN CYSTEINE-77 AND CYSTEINE-95 | ||||||
Components | HUMAN LYSOZYME | ||||||
Keywords | HYDROLASE(O-GLYCOSYL) | ||||||
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 / Resolution: 1.8 Å | ||||||
Authors | Inaka, K. / Matsushima, M. / Kuroki, R. / Taniyama, Y. / Kikuchi, M. | ||||||
Citation | Journal: Biochemistry / Year: 1992 Title: Enthalpic destabilization of a mutant human lysozyme lacking a disulfide bridge between cysteine-77 and cysteine-95. Authors: Kuroki, R. / Inaka, K. / Taniyama, Y. / Kidokoro, S. / Matsushima, M. / Kikuchi, M. / Yutani, K. #1: Journal: J.Biol.Chem. / Year: 1991 Title: The Crystal Structure of a Mutant Human Lysozyme C77(Slash)95A with Increased Secretion Efficiency in Yeast Authors: Inaka, K. / Taniyama, Y. / Kikuchi, M. / Morikawa, K. / Matsushima, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lz4.cif.gz | 33.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lz4.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/1lz4 ftp://data.pdbj.org/pub/pdb/validation_reports/lz/1lz4 | 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: 14688.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61626, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.29 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 13.0 ℃ / pH: 6 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.76 Å / Lowest resolution: 9999 Å / Num. obs: 11258 / Num. measured all: 40579 / Rmerge(I) obs: 0.0556 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 1.8→5 Å Details: THE ELECTRON DENSITIES OF THE LOOP BETWEEN ALA 73 AND HIS 78 ARE VERY WEAK AND THE ATOMS OF THE LOOP HAVE LARGE B FACTORS. THEN THE LOOP CAN BE VERY FLEXIBLE.
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Refinement step | Cycle: LAST / Resolution: 1.8→5 Å
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 5 Å / Num. reflection obs: 10265 / Rfactor obs: 0.188 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |