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Yorodumi- PDB-1lzr: STRUCTURAL CHANGES OF THE ACTIVE SITE CLEFT AND DIFFERENT SACCHAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lzr | |||||||||
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Title | STRUCTURAL CHANGES OF THE ACTIVE SITE CLEFT AND DIFFERENT SACCHARIDE BINDING MODES IN HUMAN LYSOZYME CO-CRYSTALLIZED WITH HEXA-N-ACETYL-CHITOHEXAOSE AT PH 4.0 | |||||||||
Components | HUMAN LYSOZYME | |||||||||
Keywords | HYDROLASE (O-GLYCOSYL) | |||||||||
Function / homology | Function and homology information 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 / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / Resolution: 1.5 Å | |||||||||
Authors | Matsushima, M. / Inaka, K. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: Structural changes of active site cleft and different saccharide binding modes in human lysozyme co-crystallized with hexa-N-acetyl-chitohexaose at pH 4.0. Authors: Song, H. / Inaka, K. / Maenaka, K. / Matsushima, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lzr.cif.gz | 39.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lzr.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/1lzr ftp://data.pdbj.org/pub/pdb/validation_reports/lz/1lzr | 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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-Components
#1: Protein | Mass: 14720.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00695, UniProt: P61626*PLUS, lysozyme | ||
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#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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.12 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 13 ℃ / pH: 6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
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 | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 9999 Å / Num. obs: 17996 / % possible obs: 92.3 % / Num. measured all: 64767 / Rmerge(I) obs: 0.029 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.53 Å / % possible obs: 87.6 % |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.5→5 Å /
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Refinement step | Cycle: LAST / Resolution: 1.5→5 Å
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Refine LS restraints |
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LS refinement shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.6 Å / Rfactor obs: 0.17 |