+Open data
-Basic information
Entry | Database: PDB / ID: 6a4o | |||||||||
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Title | HEWL crystals soaked in 2.5M GuHCl for 20 minutes | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE / Protein Unfolding / Chemical denaturant / guanidine / Lysozyme | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Tushar, R. / Kini, R.M. / Koh, C.Y. / Hosur, M.V. | |||||||||
Citation | Journal: Int. J. Biol. Macromol. / Year: 2019 Title: X-ray crystallographic analysis of time-dependent binding of guanidine hydrochloride to HEWL: First steps during protein unfolding. Authors: Raskar, T. / Koh, C.Y. / Niebling, S. / Kini, R.M. / Hosur, M.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a4o.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a4o.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 6a4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/6a4o ftp://data.pdbj.org/pub/pdb/validation_reports/a4/6a4o | HTTPS FTP |
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-Related structure data
Related structure data | 6a4nC 6a4pC 6a4qC 193lS 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: 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-GAI / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 1.99 Å3/Da / Density % sol: 38.1 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: The concentration of the protein was 20mg/ml. The precipitant solution in the reservoir was 0.1M sodium acetate/acetic acid buffer of pH 4.6 to 5.0 containing 1.2 to 1.5M sodium chloride. ...Details: The concentration of the protein was 20mg/ml. The precipitant solution in the reservoir was 0.1M sodium acetate/acetic acid buffer of pH 4.6 to 5.0 containing 1.2 to 1.5M sodium chloride. The soaking solution was 0.1M sodium acetate/acetic acid buffer at pH 3.5 containing 1.4M NaCl, 25% v/v glycerol (as cryo-protectant) and 2.5M of guanidine hydrochloride. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→55.5 Å / Num. obs: 10110 / % possible obs: 88.34 % / Redundancy: 1.9 % / CC1/2: 0.998 / Net I/σ(I): 16.99 |
Reflection shell | Resolution: 1.755→1.817 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193L Resolution: 1.75→55.5 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.822 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.131 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.581 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→55.5 Å
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Refine LS restraints |
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