+Open data
-Basic information
Entry | Database: PDB / ID: 1ioc | ||||||
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Title | CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME, EAEA-I56T | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / amyloid / mutant / human lysozyme / stability | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Goda, S. / Takano, K. / Yamagata, Y. / Yutani, K. | ||||||
Citation | Journal: J.Biochem. / Year: 2002 Title: Elongation in a beta-structure promotes amyloid-like fibril formation of human lysozyme. Authors: Goda, S. / Takano, K. / Yamagata, Y. / Maki, S. / Namba, K. / Yutani, K. #1: Journal: Protein Eng. / Year: 2000 Title: Effect of extra N-terminal residues on the stability and folding of human lysozyme expressed in Pichia pastoris Authors: Goda, S. / Takano, K. / Yamagata, Y. / Katakura, 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 | 1ioc.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ioc.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ioc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ioc_validation.pdf.gz | 371.2 KB | Display | wwPDB validaton report |
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Full document | 1ioc_full_validation.pdf.gz | 374.2 KB | Display | |
Data in XML | 1ioc_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 1ioc_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/1ioc ftp://data.pdbj.org/pub/pdb/validation_reports/io/1ioc | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 15109.023 Da / Num. of mol.: 1 / Mutation: I56T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPIC9 / Production host: Pichia pastoris (fungus) / References: UniProt: P61626, lysozyme | ||
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#2: Chemical | #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: 3.59 Å3/Da / Density % sol: 65.77 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: cadmium, chloride, sodium acetate, PEG400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 283K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Details: Goda, S., (2000) Protein Eng., 13, 299. | |||||||||||||||||||||||||
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: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. all: 72930 / Num. obs: 9168 / % possible obs: 99.8 % / Rmerge(I) obs: 0.118 |
Reflection | *PLUS Num. measured all: 72930 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EAEA human lysozyme Resolution: 2.4→6 Å
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Refinement step | Cycle: LAST / Resolution: 2.4→6 Å
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