+Open data
-Basic information
Entry | Database: PDB / ID: 1ip4 | ||||||
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Title | G72A HUMAN LYSOZYME | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / Glycosidase / Bacteriolytic enzyme | ||||||
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 / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Takano, K. / Yamagata, Y. / Yutani, K. | ||||||
Citation | Journal: Proteins / Year: 2001 Title: Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein. Authors: Takano, K. / Yamagata, Y. / Yutani, K. #1: Journal: Proteins / Year: 2001 Title: Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme Authors: Takano, K. / Yamagata, Y. / Yutani, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ip4.cif.gz | 43.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ip4.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ip4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/1ip4 ftp://data.pdbj.org/pub/pdb/validation_reports/ip/1ip4 | HTTPS FTP |
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-Related structure data
Related structure data | 1ip1C 1ip2C 1ip3C 1ip5C 1ip6C 1ip7C 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: 14734.719 Da / Num. of mol.: 1 / Mutation: G72A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PERI8602 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61626, lysozyme |
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#2: Chemical | ChemComp-NA / |
#3: 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: 1.92 Å3/Da / Density % sol: 35.88 % | ||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: sodium phosphate, sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 23, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.8 Å / Num. all: 55173 / Num. obs: 10477 / % possible obs: 95 % / Rmerge(I) obs: 0.029 |
Reflection | *PLUS Num. measured all: 55173 |
-Processing
Software |
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Refinement | Resolution: 1.8→8 Å
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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