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- PDB-1re2: HUMAN LYSOZYME LABELLED WITH TWO 2',3'-EPOXYPROPYL BETA-GLYCOSIDE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1re2 | |||||||||
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Title | HUMAN LYSOZYME LABELLED WITH TWO 2',3'-EPOXYPROPYL BETA-GLYCOSIDE OF N-ACETYLLACTOSAMINE | |||||||||
![]() | PROTEIN (LYSOZYME) | |||||||||
![]() | LYSOZYME / MURAMIDASE / EC 3.2.1.17 / HYDROLASE(O-GLYCOSYL) / N-ACETYLLACTOSAMINE / AFFINITY LABELING | |||||||||
Function / homology | ![]() 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 / 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: Dual affinity labeling of the active site of human lysozyme with an N-acetyllactosamine derivative: first ligand assisted recognition of the second ligand. Authors: Muraki, M. / Harata, K. / Sugita, N. / Sato, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.6 KB | Display | ![]() |
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PDB format | ![]() | 28.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rezS S: Starting model for refinement |
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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 / Source: (natural) ![]() | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 37.55 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→62.3 Å / Num. obs: 5742 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 3.7 |
Reflection | *PLUS Num. measured all: 23021 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1REZ WITH SOLVENT MOLECULESOMITTED Resolution: 2.3→8 Å / Cross valid method: A POSTERIORI / σ(F): 3
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Displacement parameters | Biso mean: 19.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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