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Yorodumi- PDB-1lhm: THE CRYSTAL STRUCTURE OF A MUTANT LYSOZYME C77(SLASH)95A WITH INC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lhm | ||||||
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Title | THE CRYSTAL STRUCTURE OF A MUTANT LYSOZYME C77(SLASH)95A WITH INCREASED SECRETION EFFICIENCY IN YEAST | ||||||
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. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1991 Title: The crystal structure of a mutant human lysozyme C77/95A with increased secretion efficiency in yeast. Authors: Inaka, K. / Taniyama, Y. / Kikuchi, M. / Morikawa, K. / Matsushima, M. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 1988 Title: Role of Disulfide Bonds in Folding and Secretion of Human Lysozyme in Saccharomyces Cerevisiae Authors: Taniyama, Y. / Yamamoto, Y. / Kikuchi, N.Nakao M. / Ikehara, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lhm.cif.gz | 34.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lhm.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/1lhm ftp://data.pdbj.org/pub/pdb/validation_reports/lh/1lhm | 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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Atom site foot note | 1: THE CYS 77 - CYS 95 DISULFIDE BOND HAS BEEN DELETED IN THIS ENTRY. |
-Components
#1: Protein | Mass: 14656.562 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 / |
Compound details | THE CYS 77 - CYS 95 DISULFIDE BOND HAS BEEN DELETED IN THIS ENTRY. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.86 % | ||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 13.0 ℃ / Method: unknown / pH: 6 | ||||||||||||||||||||||||||||
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: 11241 / Num. measured all: 78240 / Rmerge(I) obs: 0.0834 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.16 / Highest resolution: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 5 Å / Num. reflection obs: 10370 / Rfactor obs: 0.163 / Rfactor Rwork: 0.163 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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