+Open data
-Basic information
Entry | Database: PDB / ID: 208l | ||||||
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Title | MUTANT HUMAN LYSOZYME C77A | ||||||
Components | LYSOZYME | ||||||
Keywords | COMPLEX (HYDROLASE (O-GLYCOSYL)/CYS) / COMPLEX (HYDROLASE (O-GLYCOSYL)-CYS) / MUTANT HUMAN LYSOZYME / HYDROLASE / COMPLEX (HYDROLASE (O-GLYCOSYL)-CYS) complex | ||||||
Function / homology | Function and homology information cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity ...cytolysis / antimicrobial humoral response / retina homeostasis / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Matsushima, M. / Song, H. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 1996 Title: A role of PDI in the reductive cleavage of mixed disulfides. Authors: Nakamura, S. / Matsushima, M. / Song, H. / Kikuchi, M. #1: 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. #2: 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. / Kikuchi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 208l.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb208l.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 208l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/08/208l ftp://data.pdbj.org/pub/pdb/validation_reports/08/208l | HTTPS FTP |
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-Related structure data
-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 / Mutation: C77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00695, UniProt: P61626*PLUS, lysozyme |
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#2: Chemical | ChemComp-CYS / |
#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: 1.96 Å3/Da / Density % sol: 37.27 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 1, 1993 / Details: MIRROR-MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE HUMAN LYSOZYME Resolution: 2.2→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |