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Yorodumi- PDB-1re2: HUMAN LYSOZYME LABELLED WITH TWO 2',3'-EPOXYPROPYL BETA-GLYCOSIDE... -
+Open data
-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 | |||||||||
Components | PROTEIN (LYSOZYME) | |||||||||
Keywords | LYSOZYME / MURAMIDASE / EC 3.2.1.17 / HYDROLASE(O-GLYCOSYL) / N-ACETYLLACTOSAMINE / AFFINITY LABELING | |||||||||
Function / homology | Function and homology information metabolic process / cytolysis / antimicrobial humoral response / retina homeostasis / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity ...metabolic process / cytolysis / antimicrobial humoral response / retina homeostasis / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Muraki, M. / Harata, K. / Sugita, N. / Sato, K. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1re2.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1re2.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 1re2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1re2_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1re2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1re2_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1re2_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/1re2 ftp://data.pdbj.org/pub/pdb/validation_reports/re/1re2 | HTTPS FTP |
-Related structure data
Related structure data | 1rezS S: Starting model for refinement |
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Similar 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: 14720.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00695, UniProt: P61626*PLUS, lysozyme | ||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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