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Yorodumi- PDB-134l: ROLE OF ARG 115 IN THE CATALYTIC ACTION OF HUMAN LYSOZYME. X-RAY ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 134l | ||||||
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Title | ROLE OF ARG 115 IN THE CATALYTIC ACTION OF HUMAN LYSOZYME. X-RAY STRUCTURE OF HIS 115 AND GLU 115 MUTANTS | ||||||
Components | HUMAN LYSOZYME | ||||||
Keywords | HYDROLASE(O-GLYCOSYL) | ||||||
Function / homology | Function and homology information antimicrobial humoral response / 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 ...antimicrobial humoral response / 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 / Resolution: 1.77 Å | ||||||
Authors | Harata, K. / Muraki, M. / Jigami, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Role of Arg115 in the catalytic action of human lysozyme. X-ray structure of His115 and Glu115 mutants. Authors: Harata, K. / Muraki, M. / Jigami, Y. #1: Journal: Eur.J.Biochem. / Year: 1989 Title: A Structural Requirement in the Subsite F of Lysozyme. The Role of Arginine 115 in Human Lysozyme Revealed by Site-Directed Mutagenesis Authors: Muraki, M. / Morikawa, M. / Jigami, Y. / Tanaka, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 134l.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb134l.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 134l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 134l_validation.pdf.gz | 413.8 KB | Display | wwPDB validaton report |
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Full document | 134l_full_validation.pdf.gz | 417.2 KB | Display | |
Data in XML | 134l_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 134l_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/34/134l ftp://data.pdbj.org/pub/pdb/validation_reports/34/134l | HTTPS FTP |
-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: 14692.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: M13 / References: UniProt: P61626, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.38 % | |||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion / Details: used seeding | |||||||||||||||
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: 1.77 Å / Num. obs: 9105 / % possible obs: 80.5 % / Num. measured all: 34053 / Rmerge(I) obs: 0.083 |
-Processing
Software |
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Refinement | Resolution: 1.77→10 Å / Rfactor Rwork: 0.183 / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.77 Å / Lowest resolution: 10 Å / Num. reflection obs: 7455 / σ(F): 3 / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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