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Yorodumi- PDB-7fgu: H/D exchanged Hen egg-white lysozyme denatured in basic condition... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fgu | ||||||
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Title | H/D exchanged Hen egg-white lysozyme denatured in basic conditions and refolded in solution | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / H/D exchange / denatured and refolded | ||||||
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 / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kita, A. / Morimoto, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Mol Biotechnol. / Year: 2022 Title: Hydrogen/Deuterium Exchange Behavior During Denaturing/Refolding Processes Determined in Tetragonal Hen Egg-White Lysozyme Crystals. Authors: Kita, A. / Morimoto, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fgu.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fgu.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 7fgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fgu_validation.pdf.gz | 373.7 KB | Display | wwPDB validaton report |
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Full document | 7fgu_full_validation.pdf.gz | 373.8 KB | Display | |
Data in XML | 7fgu_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 7fgu_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/7fgu ftp://data.pdbj.org/pub/pdb/validation_reports/fg/7fgu | HTTPS FTP |
-Related structure data
Related structure data | 7fg8C 7fgvC 6k8gS 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: 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-CL / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: NACL, SODIUM ACETATE-D3, ACETIC ACID-D4, 100% D2O, PH 4.6 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Biso Wilson estimate: 23.04 Å2 / Entry-ID: 7FGU
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Reflection shell |
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Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | SU ML: 0.1628 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 16.842 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 6K8G / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL
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Refinement step | Cycle: LAST / Resolution: 2→39.63 Å
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Refine LS restraints |
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LS refinement shell |
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