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Yorodumi- PDB-1lsy: CRYSTAL STRUCTURE OF THE MUTANT D52S HEN EGG WHITE LYSOZYME WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lsy | ||||||
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Title | CRYSTAL STRUCTURE OF THE MUTANT D52S HEN EGG WHITE LYSOZYME WITH AN OLIGOSACCHARIDE PRODUCT | ||||||
Components | HEN EGG WHITE LYSOZYME | ||||||
Keywords | HYDROLASE(O-GLYCOSYL) | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Johnson, L.N. / Hadfield, A.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: Crystal structure of the mutant D52S hen egg white lysozyme with an oligosaccharide product. Authors: Hadfield, A.T. / Harvey, D.J. / Archer, D.B. / MacKenzie, D.A. / Jeenes, D.J. / Radford, S.E. / Lowe, G. / Dobson, C.M. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lsy.cif.gz | 36.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lsy.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/1lsy ftp://data.pdbj.org/pub/pdb/validation_reports/ls/1lsy | 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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Atom site foot note | 1: TWO ALTERNATIVE CONFORMATIONS MODELLED FOR RESIDUE VAL 109. |
-Components
#1: Protein | Mass: 16229.650 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Organ: EGG / References: UniProt: P00698, 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: 1.82 Å3/Da / Density % sol: 32.45 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 16 ℃ / pH: 4.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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 | Resolution: 2→8 Å / Num. obs: 9294 / % possible obs: 93 % |
Reflection | *PLUS Num. measured all: 17206 / Rmerge(I) obs: 0.064 |
-Processing
Software |
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Refinement | Resolution: 1.9→8 Å / σ(F): 0 /
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Displacement parameters | Biso mean: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.9 |