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Yorodumi- PDB-1hnl: CRYSTAL STRUCTURE OF A GLUTATHIONYLATED HUMAN LYSOZYME: A FOLDING... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hnl | ||||||
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Title | CRYSTAL STRUCTURE OF A GLUTATHIONYLATED HUMAN LYSOZYME: A FOLDING INTERMEDIATE MIMIC IN THE FORMATION OF A DISULFIDE BOND | ||||||
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. / Miki, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Structure of a glutathionylated human lysozyme: a folding intermediate mimic in the formation of a disulfide bond. Authors: Inaka, K. / Miki, K. / Kikuchi, M. / Taniyama, Y. / Matsushima, M. #1: Journal: FEBS Lett. / Year: 1993 Title: Pdi and Glutathione-Mediated Reduction of the Glutathionylated Variant of Human Lysozyme Authors: Hayano, T. / Inaka, K. / Otsu, M. / Taniyama, Y. / Miki, K. / Matsushima, M. / Masakazu, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hnl.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hnl.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/1hnl ftp://data.pdbj.org/pub/pdb/validation_reports/hn/1hnl | 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: Chemical | ChemComp-GSH / |
#3: Water | ChemComp-HOH / |
Source details | THE EXPRESSION PLASMID OF THE MUTANT HUMAN LYSOZYME, C77A, IN WHICH CYS 77 IS REPLACED BY ALA, WAS ...THE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.59 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 293 K / pH: 6 / Method: unknown / Details: using macroseeding | ||||||||||||||||||||||||
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 | Num. obs: 9501 / % possible obs: 84 % |
Reflection | *PLUS Highest resolution: 1.76 Å / Lowest resolution: 9999 Å / Num. measured all: 30257 / Rmerge(I) obs: 0.0667 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→5 Å /
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Displacement parameters | Biso mean: 18.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→5 Å
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Refine LS restraints |
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