+Open data
-Basic information
Entry | Database: PDB / ID: 4yop | ||||||
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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 / Resolution: 2.1 Å | ||||||
Authors | Sugahara, M. / Nakane, T. / Suzuki, M. / Nango, E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Native sulfur/chlorine SAD phasing for serial femtosecond crystallography Authors: Nakane, T. / Song, C. / Suzuki, M. / Nango, E. / Kobayashi, J. / Masuda, T. / Inoue, S. / Mizohata, E. / Nakatsu, T. / Tanaka, T. / Tanaka, R. / Shimamura, T. / Tono, K. / Joti, Y. / ...Authors: Nakane, T. / Song, C. / Suzuki, M. / Nango, E. / Kobayashi, J. / Masuda, T. / Inoue, S. / Mizohata, E. / Nakatsu, T. / Tanaka, T. / Tanaka, R. / Shimamura, T. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Nureki, O. / Iwata, S. / Sugahara, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yop.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yop.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 4yop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/4yop ftp://data.pdbj.org/pub/pdb/validation_reports/yo/4yop | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Experimental dataset #1 | Data reference: 10.11577/1236754 / Data set type: diffraction image 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-NA / |
#3: Chemical | ChemComp-CL / |
#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: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 3 / Details: sodium chloride, PEG 6000 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Jan 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 15532 / % possible obs: 100 % / Redundancy: 1119 % / Net I/σ(I): 24.9 |
-Processing
Software |
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Refinement | Resolution: 2.1→28.001 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.25 / Stereochemistry target values: ML Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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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: 2.1→28.001 Å
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Refine LS restraints |
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LS refinement shell |
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