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Yorodumi- PDB-5fhw: Hen Egg-White Lysozyme (HEWL) complexed with Hf(IV)-substituted W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fhw | ||||||
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Title | Hen Egg-White Lysozyme (HEWL) complexed with Hf(IV)-substituted Wells Dawson-type polyoxometalate | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Complex / polyoxometalate / hafnium / Wells Dawson | ||||||
Function / homology | Function and homology information Lactose synthesis / 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 ...Lactose synthesis / 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 / molecular replacement / Resolution: 1.52 Å | ||||||
Authors | Vandebroek, L. / De Zitter, E. / Van Meervelt, L. | ||||||
Citation | Journal: To Be Published Title: Structural Characterization of the Complex between Hen Egg- White Lysozyme and HfIV-Substituted Wells Dawson Polyoxometalate as Artificial Protease Authors: Vandebroek, L. / De Zitter, E. / 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 | 5fhw.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fhw.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/5fhw ftp://data.pdbj.org/pub/pdb/validation_reports/fh/5fhw | HTTPS FTP |
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-Related structure data
Related structure data | 2vb1S 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: 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-HFW / | ||
#3: Chemical | #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 Å3/Da / Density % sol: 38.45 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25 mg/mL Lysozyme C, 1.45 mM 1:2 Hf-Wells Dawson, 2.0 M sodium chloride, 0.1 M potassium phosphate monobasic, 0.1 M sodium phosphate monobasic monohydrate, 0.1 M MES pH = 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 23, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.52→39.48 Å / Num. all: 130169 / Num. obs: 18463 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.048 / Net I/σ(I): 17.3 / Num. measured all: 130169 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VB1 Resolution: 1.52→35.308 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.97 Å2 / Biso mean: 19.2414 Å2 / Biso min: 9.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.52→35.308 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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