+Open data
-Basic information
Entry | Database: PDB / ID: 1i1z | ||||||
---|---|---|---|---|---|---|---|
Title | MUTANT HUMAN LYSOZYME (Q86D) | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / CALCIUM BINDING SITE / MUTANT HUMAN LYSOZYME | ||||||
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: 1.8 Å | ||||||
Authors | Kuroki, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Structural and thermodynamic responses of mutations at a Ca2+ binding site engineered into human lysozyme. Authors: Kuroki, R. / Yutani, K. #1: Journal: J.Biol.Chem. / Year: 1992 Title: Thermodynamic changes in the binding of Ca2+ to a mutant human lysozyme (D86/92). Enthalpy-entropy compensation observed upon Ca2+ binding to proteins. Authors: Kuroki, R. / Nitta, K. / Yutani, K. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Entropic Stabilization of a Mutant Human Lysozyme Induced by Calcium Binding Authors: Kuroki, R. / Kawakita, S. / Nakamura, H. / Yutani, K. #3: Journal: J.Biol.Chem. / Year: 1991 Title: Crystal Structure of the Apo- and Holomutant Human Lysozymes with an Introduced Ca2+ Binding Site Authors: Inaka, K. / Kuroki, R. / Kikuchi, M. / Matsushima, M. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989 Title: Design and Creation of a Ca2+ Binding Site in Human Lysozyme to Enhance Structural Stability Authors: Kuroki, R. / Taniyam, Y. / Seko, C. / Nakamura, H. / Kikuchi, M. / Ikehara, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1i1z.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1i1z.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 1i1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i1z_validation.pdf.gz | 367.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1i1z_full_validation.pdf.gz | 372.9 KB | Display | |
Data in XML | 1i1z_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1i1z_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i1z ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i1z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14707.652 Da / Num. of mol.: 1 / Mutation: Q86D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PERI8811 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AH22R- References: UniProt: P61626, deoxyribodipyrimidine endonucleosidase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.88 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PHOSPHATE, SODIUM CHLORIDE, CALCIUM CHLORIDE, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: unknown | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 43723 / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 9999 Å / Num. obs: 11872 / Num. measured all: 43723 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: WILD TYPE HUMAN LYSOZYME Resolution: 1.8→20 Å / σ(F): 0 / σ(I): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|