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Yorodumi- PDB-1lz5: STRUCTURAL AND FUNCTIONAL ANALYSES OF THE ARG-GLY-ASP SEQUENCE IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lz5 | ||||||
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Title | STRUCTURAL AND FUNCTIONAL ANALYSES OF THE ARG-GLY-ASP SEQUENCE INTRODUCED INTO HUMAN LYSOZYME | ||||||
Components | HUMAN LYSOZYME | ||||||
Keywords | HYDROLASE(O-GLYCOSYL) | ||||||
Function / homology | Function and homology information antimicrobial humoral response / 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 ...antimicrobial humoral response / 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: 1.8 Å | ||||||
Authors | Matsushima, M. / Inaka, K. / Yamada, T. / Sekiguchi, K. / Kikuchi, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1993 Title: Structural and functional analyses of the Arg-Gly-Asp sequence introduced into human lysozyme. Authors: Yamada, T. / Matsushima, M. / Inaka, K. / Ohkubo, T. / Uyeda, A. / Maeda, T. / Titani, K. / Sekiguchi, K. / Kikuchi, M. #1: Journal: Science / Year: 1992 Title: Structure of a Fibronectin Type III Domain from Tenascin Phased by MAD Analysis of the Selenomethionyl Protein Authors: Leahy, D.J. / Hendrickson, W.A. / Aukhil, I. / Erickson, H.P. #2: Journal: J.Biol.Chem. / Year: 1991 Title: The Crystal Structure of a Mutant Human Lysozyme C77(Slash)95A with Increased Secretion Efficiency in Yeast Authors: Inaka, K. / Taniyama, Y. / Kikuchi, M. / Morikawa, 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 | 1lz5.cif.gz | 36.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lz5.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/1lz5 ftp://data.pdbj.org/pub/pdb/validation_reports/lz/1lz5 | 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: 15137.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61626, lysozyme | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.14 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 13.0 ℃ / pH: 6 / Method: unknown | ||||||||||||||||||||||||
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: 1.8 Å / Num. obs: 10744 / Rmerge(I) obs: 0.038 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→5 Å /
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Refinement step | Cycle: LAST / Resolution: 1.8→5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 5 Å / Num. reflection obs: 10744 / Rfactor obs: 0.146 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |