SASDA96: Lysozyme (Lysozyme C, Lysozyme, lys)

Basic information

• Entry: Database: SASBDB / ID: SASDA96

Sample

Lysozyme

• Lysozyme C (protein), Lysozyme, lys, Gallus gallus

Function / homology

Function:

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

Domain/homology:

Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily

Component:

Lysozyme C

• Biological species: Gallus gallus (chicken)
• Citation: Journal: Nat Methods / Year: 2015; Title: Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra.; Authors: Daniel Franke / Cy M Jeffries / Dmitri I Svergun / ; Abstract: Assessing similarity between data sets with the reduced χ(2) test requires the estimation of experimental errors, which, if incorrect, may render statistical comparisons invalid. We report a goodness-of-fit test, Correlation Map (CorMap), for assessing differences between one-dimensional spectra independently of explicit error estimates, using only data point correlations. Using small-angle X-ray scattering data, we demonstrate that CorMap maintains the power of the reduced χ(2) test; moreover, CorMap is also applicable to other physical experiments.

Contact author

• Dmitri Svergun
• Cy M Jeffries
• Daniel Franke

Models

• Model #167: ; Type: dummy / Radius of dummy atoms: 1.90 A / Chi-square value: 0.958441; Search similar-shape structures of this assembly by Omokage search (details)
• Model #168: ; Type: atomic / Chi-square value: 0.9604; Search similar-shape structures of this assembly by Omokage search (details)
• Model #169: ; Type: atomic / Chi-square value: 0.976144; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Lysozyme / Ext coefficient: 2.653 / Specimen concentration: 2.61 mg/ml
• Buffer: Name: 20 mM Sodium Acetate/HEPES / Concentration: 20.00 mM / pH: 6.8 / Comment: Mixed Buffer

Entity #119

Name: Lysozyme, lys / Type: protein / Description: Lysozyme C / Formula weight: 14.31 / Num. of mol.: 1 / Source: Gallus gallus / References: UniProt: P00698
Sequence:

KVFGRCELAA AMKRHGLDNY RGYSLGNWVC AAKFESNFNT QATNRNTDGS TDYGILQINS RWWCNDGRTP GSRNLCNIPC SALLSSDITA SVNCAKKIVS DGNGMNAWVA WRNRCKGTDV QAWIRGCRL

Experimental information

• Beam: Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: lysozyme pH 6.8 / Measurement date: Feb 17, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.1662	3.7891

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 456 /

	Min	Max
Q	0.1689	3.789
P(R) point	1	456
R	0	4.79

Result

Type of curve: single_conc / Standard: Bovine Serum Albumin

	Experimental	Standard	Porod
MW	14.8 kDa	14.8 kDa	13.93 kDa
Volume	-	-	23.69 nm3

	P(R)	Guinier
Forward scattering, I0	780.5	779.5
Radius of gyration, Rg	1.51 nm	1.5 nm

	Min	Max
D	-	4.79
Guinier point	1	260