+Open data
-Basic information
Entry | Database: PDB / ID: 4xjf | |||||||||||||||
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Title | X-ray structure of Lysozyme B1 | |||||||||||||||
Components | Lysozyme C | |||||||||||||||
Keywords | HYDROLASE / muramidase / N-acetylmuramide glycanhydrolase | |||||||||||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | |||||||||||||||
Authors | Huang, C.Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M. | |||||||||||||||
Funding support | Ireland, United States, 4items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xjf.cif.gz | 36.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xjf.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/4xjf ftp://data.pdbj.org/pub/pdb/validation_reports/xj/4xjf | HTTPS FTP |
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-Related structure data
Related structure data | 4xjbC 4xjdC 4xjgC 4xjhC 4xjiC 4xniC 4xnjC 4xnkC 4xnlC C: citing same article (ref.) |
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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 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) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.41 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 1M NaBr, 50-100 mM CH3COONa, pH4.5, 15-30% pEG 400 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.92049 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92049 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 11797 / % possible obs: 99.9 % / Redundancy: 32.3 % / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 33.2 % / Mean I/σ(I) obs: 3.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→39.55 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.55 / 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: 1.8→39.55 Å
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Refine LS restraints |
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LS refinement shell |
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