+Open data
-Basic information
Entry | Database: PDB / ID: 7knk | |||||||||
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Title | STRUCTURE OF HEN EGG-WHITE LYSOZYME grown with Kitchen recipe | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE / Lysozyme / kitchen recipe | |||||||||
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 / Resolution: 1.45 Å | |||||||||
Authors | Fox, A.L. / Mathews, I.I. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: STRUCTURE OF HEN EGG-WHITE LYSOZYME grown with Kitchen recipe Authors: Fox, A.L. / Mathews, I.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7knk.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7knk.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 7knk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7knk_validation.pdf.gz | 408.6 KB | Display | wwPDB validaton report |
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Full document | 7knk_full_validation.pdf.gz | 408.6 KB | Display | |
Data in XML | 7knk_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 7knk_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/7knk ftp://data.pdbj.org/pub/pdb/validation_reports/kn/7knk | HTTPS FTP |
-Related structure data
Related structure data | 193lS 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 genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-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: 38.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 / Details: Rice vinegar, Common salt and Baking powder |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.195 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2020 Details: Rh coated collimating mirror, Toroidal focusing mirror | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.195 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→39.27 Å / Num. obs: 21165 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.017 / Rrim(I) all: 0.058 / Net I/σ(I): 24.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 193l Resolution: 1.45→39.27 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.917 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.88 Å2 / Biso mean: 20.431 Å2 / Biso min: 6.8 Å2
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Refinement step | Cycle: final / Resolution: 1.45→39.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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