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Open data
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Basic information
Entry | Database: PDB / ID: 1ckg | ||||||
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Title | T52V MUTANT HUMAN LYSOZYME | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / STABILITY / HYDROGEN BOND | ||||||
Function / homology | ![]() antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / 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 | ![]() ![]() | ||||||
![]() | Takano, K. / Yamagata, Y. / Funahashi, J. / Yutani, K. | ||||||
![]() | ![]() Title: Contribution of intra- and intermolecular hydrogen bonds to the conformational stability of human lysozyme(,). Authors: Takano, K. / Yamagata, Y. / Funahashi, J. / Hioki, Y. / Kuramitsu, S. / Yutani, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.9 KB | Display | ![]() |
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PDB format | ![]() | 51.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 368.5 KB | Display | ![]() |
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Full document | ![]() | 371.5 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cj6C ![]() 1cj7C ![]() 1cj8C ![]() 1cj9C ![]() 1ckcC ![]() 1ckdC ![]() 1ckfC ![]() 1ckhC 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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Unit cell |
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Components
#1: Protein | Mass: 14718.719 Da / Num. of mol.: 2 / Mutation: T52V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.37 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.2 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 / Method: vapor diffusion, hanging dropDetails: protein solution is mixed in a 1:1 ratio with well solution | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 16216 / % possible obs: 83.6 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 2→2.09 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.3 / % possible all: 61.1 |
Reflection | *PLUS Num. measured all: 31949 |
Reflection shell | *PLUS % possible obs: 61.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: WILD-TYPE OF HUMAN LYSOZYME Resolution: 2.2→8 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.29 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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