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Yorodumi- PDB-1uia: ANALYSIS OF THE STABILIZATION OF HEN LYSOZYME WITH THE HELIX DIPO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uia | ||||||
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Title | ANALYSIS OF THE STABILIZATION OF HEN LYSOZYME WITH THE HELIX DIPOLE AND CHARGED SIDE CHAINS | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / ELECTROSTATIC INTERACTION / HELIX / HEN LYSOZYME / STABILITY | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.76 Å | ||||||
Authors | Motoshima, H. / Ohmura, T. / Ueda, T. / Imoto, T. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2002 Title: Fluctuations in free or substrate-complexed lysozyme and a mutant of it detected on x-ray crystallography and comparison with those detected on NMR. Authors: Ohmura, T. / Motoshima, H. / Ueda, T. / Imoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uia.cif.gz | 33.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uia.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 1uia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/1uia ftp://data.pdbj.org/pub/pdb/validation_reports/ui/1uia | HTTPS FTP |
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-Related structure data
Related structure data | 1uibC 1uihC 1rfpS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 14035.819 Da / Num. of mol.: 1 / Mutation: DEL(14,15) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: HEN LYSOZYME / Gene (production host): HEN LYSOZYME / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): SACCHAROMYCES CEREVISIAE / References: UniProt: P00698, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.88 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.7 / Details: 50 MM ACETATE AT PH 4.7 CONTAINING 0.9 M NACL | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 30, 1995 / Details: CU KA |
Radiation | Monochromator: MIRROR-MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→100 Å / Num. obs: 10820 / % possible obs: 86.2 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.0483 |
Reflection shell | Resolution: 1.757→1.81 Å / Rmerge(I) obs: 0.284 / % possible all: 59.8 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1RFP Resolution: 1.76→6 Å / Data cutoff low absF: 1 / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.76→6 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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