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Open data
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Basic information
Entry | Database: PDB / ID: 1rez | |||||||||
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Title | HUMAN LYSOZYME-N-ACETYLLACTOSAMINE COMPLEX | |||||||||
![]() | LYSOZYME | |||||||||
![]() | HYDROLASE (O-GLYCOSYL) / GLYCOSYDASE / VERTEBRATE C-TYPE | |||||||||
Function / homology | ![]() cytolysis / antimicrobial humoral response / retina homeostasis / metabolic process / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity ...cytolysis / antimicrobial humoral response / retina homeostasis / metabolic process / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Muraki, M. / Harata, K. / Sugita, N. / Sato, K. | |||||||||
![]() | ![]() Title: Origin of carbohydrate recognition specificity of human lysozyme revealed by affinity labeling. Authors: Muraki, M. / Harata, K. / Sugita, N. / Sato, K. #1: ![]() Title: Dissection of the Functional Role of Structural Elements of Tyrosine-63 in the Catalytic Action of Human Lysozyme Authors: Muraki, M. / Harata, K. / Jigami, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.5 KB | Display | ![]() |
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PDB format | ![]() | 27.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.8 KB | Display | ![]() |
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Full document | ![]() | 442.8 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rexC ![]() 1reyC ![]() 1lz1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14720.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: HUMAN LYSOZYME, PH 4.5, N-ACETYLLACTOSAMINE COVALENTLY ATTACHED TO ASP 53 VIA AN ESTER BOND Source: (natural) ![]() |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: Muraki, M., (1991) Biochim. Biophys. Acta 1079, 229. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→14.7 Å / Num. obs: 12070 / % possible obs: 76.9 % / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Rmerge(I) obs: 0.049 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NATIVE HUMAN LYSOZYME (PDB ENTRY 1LZ1) Resolution: 1.7→8 Å / σ(F): 3
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Displacement parameters | Biso mean: 20.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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