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Yorodumi- PDB-5fel: Hen egg lysozyme at room temperature solved from dataset acquired... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fel | ||||||
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Title | Hen egg lysozyme at room temperature solved from dataset acquired by oscillation method | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE | ||||||
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: 1.8 Å | ||||||
Authors | Tsujino, S. / Tomizaki, T. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature. Authors: Tsujino, S. / Tomizaki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fel.cif.gz | 40.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fel.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/5fel ftp://data.pdbj.org/pub/pdb/validation_reports/fe/5fel | HTTPS FTP |
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-Related structure data
Related structure data | 5fdjC 5fekC 4xjbS S: Starting model for refinement 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
#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 | #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: 41.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Na acetate, MPEG 5K, NaCl, Na acetate, ethylene glycerol PH range: 4.4-4.6 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 477708 / Num. obs: 72771 / % possible obs: 99.9 % / Redundancy: 6.56 % / Rmerge(I) obs: 0.063 / Rsym value: 0.058 / Net I/σ(I): 11.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XJB Resolution: 1.8→40.01 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.893 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.79 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→40.01 Å
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Refine LS restraints |
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