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Yorodumi- PDB-6hyb: Zr(IV)-substituted Wells-Dawson binding to Hen Egg-White Lysozyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hyb | ||||||
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Title | Zr(IV)-substituted Wells-Dawson binding to Hen Egg-White Lysozyme (HEWL) | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Lysozyme / co-crystal / polyoxometalate / catalysis | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 / molecular replacement / Resolution: 1.964 Å | ||||||
Authors | Vandebroek, L. / Van Meervelt, L. / Parac-Vogt, T.N. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Eur J Inorg Chem / Year: 2019 Title: Noncovalent Complexes Formed between Metal-Substituted Polyoxometalates and Hen Egg White Lysozyme Authors: Vandebroek, L. / Mampaey, Y. / Antonyuk, S. / Van Meervelt, L. / Parac-Vogt, T.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hyb.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hyb.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 6hyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hyb_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6hyb_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6hyb_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 6hyb_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/6hyb ftp://data.pdbj.org/pub/pdb/validation_reports/hy/6hyb | HTTPS FTP |
-Related structure data
Related structure data | 6hy4C 6hy6C 6hy8C 1lyzS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14218.001 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-ZRW / |
#3: Chemical | ChemComp-K / |
#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: 2.02 Å3/Da / Density % sol: 38.99 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 4 Details: 1.75 mM HEWL, 0.8 mM 1:1 Zr(IV)-Wells-Dawson, 1 M LiCl, 30% PEG 6000, 0.1 M Citric acid pH = 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→35.16 Å / Num. obs: 15576 / % possible obs: 98.6 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.89 |
Reflection shell | Resolution: 1.96→2.08 Å / Rmerge(I) obs: 0.806 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 1LYZ Resolution: 1.964→35.155 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 25.08 / Details: Phenix.refine v 1.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.03 Å2 / Biso mean: 39.0864 Å2 / Biso min: 0.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.964→35.155 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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