[English] 日本語
Yorodumi- PDB-154l: THE REFINED STRUCTURES OF GOOSE LYSOZYME AND ITS COMPLEX WITH A B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 154l | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | THE REFINED STRUCTURES OF GOOSE LYSOZYME AND ITS COMPLEX WITH A BOUND TRISACCHARIDE SHOW THAT THE "GOOSE-TYPE LYSOZYMES LACK A CATALYTIC ASPARTATE | |||||||||
Components | GOOSE LYSOZYME | |||||||||
Keywords | HYDROLASE(O-GLYCOSYL) | |||||||||
Function / homology | Function and homology information peptidoglycan catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / extracellular region Similarity search - Function | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | |||||||||
Authors | Weaver, L.H. / Gruetter, M.G. / Matthews, B.W. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: The refined structures of goose lysozyme and its complex with a bound trisaccharide show that the "goose-type" lysozymes lack a catalytic aspartate residue. Authors: Weaver, L.H. / Grutter, M.G. / Matthews, B.W. #1: Journal: J.Mol.Biol. / Year: 1987 Title: The Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution Authors: Weaver, L.H. / Matthews, B.W. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 154l.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb154l.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 154l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/54/154l ftp://data.pdbj.org/pub/pdb/validation_reports/54/154l | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20406.139 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P00718, lysozyme |
---|---|
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.67 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.6 / Method: batch method | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.6 Å / Num. obs: 21303 / % possible obs: 74 % / Num. measured all: 72401 / Rmerge F obs: 0.074 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.6→6 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→6 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.159 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_d / Dev ideal: 2.5 |