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Yorodumi- PDB-5i4x: Exploring onset of lysozyme denaturation by urea - soak period 2 hours -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i4x | ||||||
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Title | Exploring onset of lysozyme denaturation by urea - soak period 2 hours | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Lysozyme / urea / denaturation | ||||||
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 / Resolution: 1.607 Å | ||||||
Authors | Hosur, M.V. / Raskar, T. / Khavnekar, S. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation Authors: Raskar, T. / Khavnekar, S. / Hosur, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i4x.cif.gz | 39.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i4x.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 5i4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/5i4x ftp://data.pdbj.org/pub/pdb/validation_reports/i4/5i4x | HTTPS FTP |
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-Related 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-URE / #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: 38.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: Sodium chloride, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.607→30.73 Å / Num. obs: 15398 / % possible obs: 98.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0365 / Net I/σ(I): 14.29 |
-Processing
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Refinement | Resolution: 1.607→30.73 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.607→30.73 Å
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Refine LS restraints |
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LS refinement shell |
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