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Yorodumi- PDB-3wvy: Structure of D48A hen egg white lysozyme in complex with (GlcNAc)4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wvy | |||||||||
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Title | Structure of D48A hen egg white lysozyme in complex with (GlcNAc)4 | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE / Hydrolase (O-glycosyl) / Sugar Binding | |||||||||
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: 1.56 Å | |||||||||
Authors | Kawaguchi, Y. / Yoneda, K. / Araki, T. | |||||||||
Citation | Journal: TO BE PUBLISHED Title: The role of Asp48 in the hydrogen bonding network involving Asp52 of hen egg white lysozyme Authors: Kawaguchi, Y. / Yoneda, K. / Araki, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wvy.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wvy.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/3wvy ftp://data.pdbj.org/pub/pdb/validation_reports/wv/3wvy | HTTPS FTP |
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-Related structure data
Related structure data | 3wvxC 1lzcS 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: 14287.150 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Mutation: D48A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P00698, lysozyme |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: 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 Å3/Da / Density % sol: 38.4 % |
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Crystal grow | Temperature: 293 K / pH: 4 Details: 0.1M Sodium acetate buffer, 1.2M NaCl, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→50 Å / Num. obs: 17024 / Biso Wilson estimate: 20.73 Å2 |
Reflection shell | Resolution: 1.56→50 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LZC Resolution: 1.56→31.34 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.872 / SU B: 1.463 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.108 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→31.34 Å
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