|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 / cell wall macromolecule catabolic process / killing of cells of other organism / lysozyme / lysozyme activity / 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 / Lowest resolution: 10 / 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 / R factor R free: 0.729 / R factor R work: 0.532 / Lowest resolution: 2.14 / Number reflection R free: 10 / Number reflection R work: 307 / Percent reflection obs: 10.47|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi