+Open data
-Basic information
Entry | Database: PDB / ID: 3wxt | ||||||
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Title | Crystal structure of hen egg-white lysozyme | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / serial femtosecond crystallography | ||||||
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 / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Sugahara, M. / Nango, E. / Suzuki, M. | ||||||
Citation | Journal: Nat.Methods / Year: 2015 Title: Grease matrix as a versatile carrier of proteins for serial crystallography Authors: Sugahara, M. / Mizohata, E. / Nango, E. / Suzuki, M. / Tanaka, T. / Masuda, T. / Tanaka, R. / Shimamura, T. / Tanaka, Y. / Suno, C. / Ihara, K. / Pan, D. / Kakinouchi, K. / Sugiyama, S. / ...Authors: Sugahara, M. / Mizohata, E. / Nango, E. / Suzuki, M. / Tanaka, T. / Masuda, T. / Tanaka, R. / Shimamura, T. / Tanaka, Y. / Suno, C. / Ihara, K. / Pan, D. / Kakinouchi, K. / Sugiyama, S. / Murata, M. / Inoue, T. / Tono, K. / Song, C. / Park, J. / Kameshima, T. / Hatsui, T. / Joti, Y. / Yabashi, M. / Iwata, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wxt.cif.gz | 36.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wxt.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/3wxt ftp://data.pdbj.org/pub/pdb/validation_reports/wx/3wxt | HTTPS FTP |
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-Related structure data
Related structure data | 3wulC 3wumC 3wxqC 3wxsC 3wxuC 4w4qC 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 | ChemComp-NA / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 14595 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.54 % |
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Crystal grow | Temperature: 293 K / Method: batch / pH: 3 Details: sodium chloride, PEG 6000, pH 3.0, batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å |
Detector | Type: MPCCD octal / Detector: CCD / Date: Dec 9, 2013 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 8549 / Num. obs: 8549 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.04 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→27.93 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.605 Å2
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Refinement step | Cycle: LAST / Resolution: 2→27.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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