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- PDB-1lz6: STRUCTURAL AND FUNCTIONAL ANALYSES OF THE ARG-GLY-ASP SEQUENCE IN... -
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Basic information
Entry | Database: PDB / ID: 1lz6 | ||||||
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Title | STRUCTURAL AND FUNCTIONAL ANALYSES OF THE ARG-GLY-ASP SEQUENCE INTRODUCED INTO HUMAN LYSOZYME | ||||||
![]() | HUMAN LYSOZYME | ||||||
![]() | HYDROLASE(O-GLYCOSYL) | ||||||
Function / homology | ![]() antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Matsushima, M. / Inaka, K. / Yamada, T. / Sekiguchi, K. / Kikuchi, M. | ||||||
![]() | ![]() 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: ![]() Title: Structure of a Fibronectin Typeiii Domain from Tenascin Phased by MAD Analysis of the Selenomethionyl Protein Authors: Leahy, D.J. / Hendrickson, W.A. / Aukhil, I. / Erickson, H.P. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 39.2 KB | Display | ![]() |
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PDB format | ![]() | 30 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.1 KB | Display | ![]() |
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Full document | ![]() | 420.6 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 15463.455 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.71 % | ||||||||||||||||||||||||
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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: 10586 / Rmerge(I) obs: 0.056 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→6 Å Details: THE ELECTRON DENSITY MAP WITHOUT THE PHASE CONTRIBUTION OF RESIDUES ALA 73, VAL 74 AND THE INSERTED AMINO ACIDS DID NOT SHOW SIGNIFICANT ELECTRON DENSITIES FOR THE RESIDUES FROM ALA 73 TO ...Details: THE ELECTRON DENSITY MAP WITHOUT THE PHASE CONTRIBUTION OF RESIDUES ALA 73, VAL 74 AND THE INSERTED AMINO ACIDS DID NOT SHOW SIGNIFICANT ELECTRON DENSITIES FOR THE RESIDUES FROM ALA 73 TO PRO 74G, BUT THE MAP CLEARLY SHOWED THE ELECTRON DENSITY OF ALA 74H. THE REFINED B FACTORS OF THE RESIDUES ALA 73 TO PRO 74G ARE LARGE WITH POORLY DEFINED POSITIONAL PARAMETERS.
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Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 10586 / Rfactor obs: 0.152 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |