+Open data
-Basic information
Entry | Database: PDB / ID: 6fsj | ||||||
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Title | Crystal structure of TCE-treated Lysozyme | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / TCE-treatment / Lysozyme | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Pichlo, C. / Baumann, U. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer. Authors: Pichlo, C. / Toelzer, C. / Chojnacki, K. / Ocal, S. / Uthoff, M. / Ruegenberg, S. / Hermanns, T. / Schacherl, M. / Denzel, M.S. / Hofmann, K. / Niefind, K. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fsj.cif.gz | 93.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fsj.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/6fsj ftp://data.pdbj.org/pub/pdb/validation_reports/fs/6fsj | HTTPS FTP |
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-Related structure data
Related structure data | 5n12C 6fsmC 6breS C: citing same article (ref.) S: Starting model for refinement |
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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 | #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30 mg/ml Lysozyme in 20 mM Tris pH 7.5, 200 mM NaCl 1:1 with 1.0 M LiCl, 0.1 M Na citrate pH 4.0 20 % w/v PEG 6000 Cryoprotectant: Etylene glycol 30 mM TCE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.999 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→33.836 Å / Num. obs: 37081 / % possible obs: 99.77 % / Redundancy: 5.3 % / Net I/σ(I): 13.77 |
Reflection shell | Resolution: 1.2→1.243 Å / Redundancy: 4.9 % / Num. unique obs: 3649 / % possible all: 99.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BRE Resolution: 1.2→33.836 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 16.7 / 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: 1.2→33.836 Å
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Refine LS restraints |
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LS refinement shell |
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