|Entry||Database: PDB / ID: 6h3b|
|Title||Lysozyme: Machining protein microcrystals for structure determination by electron diffraction|
|Keywords||HYDROLASE / lysozyme / hydrolase|
|Function / homology||Lysozyme-like domain superfamily / Lysozyme C / Glycoside hydrolase, family 22, conserved site / Glycoside hydrolase, family 22 / Glycoside hydrolase, family 22, lysozyme / C-type lysozyme/alpha-lactalbumin family / Alpha-lactalbumin / lysozyme C signature. / Neutrophil degranulation / Alpha-lactalbumin / lysozyme C family profile. / Antimicrobial peptides ...Lysozyme-like domain superfamily / Lysozyme C / Glycoside hydrolase, family 22, conserved site / Glycoside hydrolase, family 22 / Glycoside hydrolase, family 22, lysozyme / C-type lysozyme/alpha-lactalbumin family / Alpha-lactalbumin / lysozyme C signature. / Neutrophil degranulation / Alpha-lactalbumin / lysozyme C family profile. / Antimicrobial peptides / catabolism by organism of cell wall peptidoglycan in other organism / beta-N-acetylglucosaminidase activity / killing of cells of other organism / lysozyme / lysozyme activity / cell wall macromolecule catabolic process / cytolysis / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm / Lysozyme C|
Function and homology information
|Specimen source||Gallus gallus (chicken)|
|Method||ELECTRON CRYSTALLOGRAPHY / electron crystallography / 1.9 Å resolution|
|Authors||Duyvesteyn, H.M.E. / Ginn, H.M. / Stuart, D.I.|
|Citation||Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018|
Title: Machining protein microcrystals for structure determination by electron diffraction.
Authors: Helen M E Duyvesteyn / Abhay Kotecha / Helen M Ginn / Corey W Hecksel / Emma V Beale / Felix de Haas / Gwyndaf Evans / Peijun Zhang / Wah Chiu / David I Stuart
Abstract: We demonstrate that ion-beam milling of frozen, hydrated protein crystals to thin lamella preserves the crystal lattice to near-atomic resolution. This provides a vehicle for protein structure ...We demonstrate that ion-beam milling of frozen, hydrated protein crystals to thin lamella preserves the crystal lattice to near-atomic resolution. This provides a vehicle for protein structure determination, bridging the crystal size gap between the nanometer scale of conventional electron diffraction and micron scale of synchrotron microfocus beamlines. The demonstration that atomic information can be retained suggests that milling could provide such detail on sections cut from vitrified cells.
SummaryFull reportAbout validation report
|Date||Deposition: Jul 18, 2018 / Release: Sep 12, 2018|
|Structure viewer||Molecule: |
Downloads & links
A: Lysozyme C
|#1: Protein/peptide|| |
Mass: 14331.160 Da / Num. of mol.: 1 / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
|#2: Chemical|| ChemComp-CL / |
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: ELECTRON CRYSTALLOGRAPHY|
|EM experiment||Aggregation state: 3D ARRAY / Reconstruction method: electron crystallography|
|Component||Name: lysozyme / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: NATURAL|
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Gallus gallus (chicken)|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO|
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TALOS ARCTICA|
|Electron gun||Illumination mode: OTHER|
|Electron lens||Mode: DIFFRACTION|
|Refine||R Free selection details: Copied from 5wr9.pdb / Cross valid method: FREE R-VALUE|
|Least-squares process||R factor R free: 0.283 / R factor R work: 0.291 / Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Number reflection R free: 313 / Number reflection obs: 3508 / Percent reflection R free: 5 / Percent reflection obs: 38.67|
|Refine LS restraints||Type: Rigid body|
|Refine LS shell||Highest resolution: 1.9 Å / R factor R free: 0.729 / R factor R work: 0.532 / Lowest resolution: 2.14 Å / Number reflection R free: 10 / Number reflection R work: 307 / Percent reflection obs: 10.47|
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