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- SASDAG2: Lyz in Sodium Acetate (Lysozyme C, Lys) -

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Open data


ID or keywords:

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Basic information

Entry
Database: SASBDB / ID: SASDAG2
SampleLyz in Sodium Acetate
  • Lysozyme C (protein), Lys, Gallus gallus
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
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
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
Contact author
  • Darja Ruskule (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #18
Type: dummy / Radius of dummy atoms: 1.90 A / Symmetry: P1
Comment: ran it 10 times and took the model with the lowest NSD (damsel) and visually best fit (pymol)
Chi-square value: 2.8561
Search similar-shape structures of this assembly by Omokage search (details)
Model #17
Type: atomic / Chi-square value: 0.844561
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Lyz in Sodium Acetate / Ext coefficient: 26.53 / Contrast: 3.047 / Specific vol: 0.7402 / Purity method: gel filtration / Dry vol: 19648 / Sample MW: 14.3 kDa / Specimen concentration: 8.09 mg/ml / Concentration method: nanodrop
BufferName: 40 mM Sodium Acetate / Concentration: 40.00 mM / pH: 3.8
Entity #14Name: Lys / Type: protein / Description: Lysozyme C / Formula weight: 16.24 / Num. of mol.: 1 / Source: Gallus gallus / References: UniProt: P00698
Sequence:
MRSLLILVLC FLPLAALGKV FGRCELAAAM KRHGLDNYRG YSLGNWVCAA KFESNFNTQA TNRNTDGSTD YGILQINSRW WCNDGRTPGS RNLCNIPCSA LLSSDITASV NCAKKIVSDG NGMNAWVAWR NRCKGTDVQA WIRGCRL

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Experimental information

BeamInstrument name: DORIS III EMBL X33 / City: Hamburg / 国: Germany / Shape: 0.6 / Type of source: X-ray synchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 2.7 mm
DetectorName: Pilatus 1M-W / Pixsize x: 0.172 mm
Scan
Title: Lyz in Sodium Acetate / Measurement date: Sep 21, 2012 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 15 sec. / Number of frames: 8 / Unit: 1/nm /
MinMax
Q0.0871 17.6902
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1739 /
MinMax
Q0.308583 5.06308
P(R) point1 1739
R0 4.06
Result
Type of curve: merged / Standard: BSA /
ExperimentalStandardPorod
MW11 kDa11 kDa-
Volume--20.7 nm3

P(R)Guinier
Forward scattering, I012.02 12.29
Radius of gyration, Rg1.43 nm1.45 nm

MinMax
D-4
Guinier point177 294

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