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Open data
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Basic information
Entry | Database: PDB / ID: 1iwv | ||||||
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Title | Crystal Structure Analysis of Human lysozyme at 147K. | ||||||
![]() | LYSOZYME C | ||||||
![]() | HYDROLASE / O-GLYCOSYL / GLYCOSYDASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Joti, Y. / Nakasako, M. / Kidera, A. / Go, N. | ||||||
![]() | ![]() Title: Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors. Authors: Joti, Y. / Nakasako, M. / Kidera, A. / Go, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123 KB | Display | ![]() |
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PDB format | ![]() | 96.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1iwtC ![]() 1iwuC ![]() 1iwwC ![]() 1iwxC ![]() 1iwyC ![]() 1iwzC C: citing same article ( |
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Similar 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: 14720.693 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: 1.93 Å3/Da / Density % sol: 36.4 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: NaCl, acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Details: Takano, K., (1995) J. Mol. Biol., 254, 62. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 147 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40 Å / Num. all: 24643 / Num. obs: 24634 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 95.9 % / Num. measured all: 236842 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 1.37 Å / % possible obs: 58.7 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 8.3 |
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Processing
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Refinement | Resolution: 1.4→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.4→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.16 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |