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Open data
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Basic information
Entry | Database: PDB / ID: 4xjd | |||||||||||||||
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Title | X-ray structure of Lysozyme2 | |||||||||||||||
![]() | Lysozyme C | |||||||||||||||
![]() | HYDROLASE / muramidase / N-acetylmuramide glycanhydrolase | |||||||||||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Huang, C.Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins. Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Panepucci, E. / Diederichs, K. / Wang, M. / Caffrey, M. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.6 KB | Display | ![]() |
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PDB format | ![]() | 26.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423 KB | Display | ![]() |
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Full document | ![]() | 424.1 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xjbC ![]() 4xjfC ![]() 4xjgC ![]() 4xjhC ![]() 4xjiC ![]() 4xniC ![]() 4xnjC ![]() 4xnkC ![]() 4xnlC ![]() 3tmuS S: Starting model for refinement 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 on special symmetry positions |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.13 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.5-1 M NaCl, 50-100 mM CH3COONa, pH4.5, and 15-30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 10805 / % possible obs: 99.6 % / Redundancy: 7 % / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TMU Resolution: 1.801→34.664 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.801→34.664 Å
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Refine LS restraints |
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LS refinement shell |
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