|Entry||Database: PDB / ID: 6drv|
|Keywords||HYDROLASE / cryo-EM / Amazon Web Services / RELION|
|Function / homology||Immunoglobulin-like fold / Galactose-binding-like domain superfamily / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Beta-galactosidase, domain 4 / Glycoside hydrolase, family 2, beta-galactosidase / Glycoside hydrolase, family 2, active site / Glycoside hydrolase, family 2, conserved site / Glycoside hydrolase superfamily / Glycoside hydrolase-type carbohydrate-binding ...Immunoglobulin-like fold / Galactose-binding-like domain superfamily / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Beta-galactosidase, domain 4 / Glycoside hydrolase, family 2, beta-galactosidase / Glycoside hydrolase, family 2, active site / Glycoside hydrolase, family 2, conserved site / Glycoside hydrolase superfamily / Glycoside hydrolase-type carbohydrate-binding / Beta galactosidase small chain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycoside hydrolase, family 2 / Beta galactosidase small chain/ domain 5 / Domain of unknown function(DUF4981) / Glycosyl hydrolases family 2 acid/base catalyst. / Glycosyl hydrolases family 2 signature 1. / Glycosyl hydrolases family 2, TIM barrel domain / alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding / Beta-galactosidase|
Function and homology information
|Specimen source||Escherichia coli (E. coli)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.2 Å resolution|
|Authors||Cianfrocco, M.A. / Lahiri, I. / DiMaio, F. / Leschziner, A.E.|
|Citation||Journal: J. Struct. Biol. / Year: 2018|
Title: cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud.
Authors: Michael A Cianfrocco / Indrajit Lahiri / Frank DiMaio / Andres E Leschziner
Abstract: Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have developed tools that will submit cryo-EM ...Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have developed tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools ("cryoem-cloud-tools") have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines. Integrating these tools into the RELION processing pipeline and graphical user interface we determined a 2.2 Å structure of ß-galactosidase in ∼55 h on AWS. We implemented a similar strategy to submit Rosetta atomic model building and refinement to AWS. These software tools dramatically reduce the barrier for entry of new users to cloud computing for cryo-EM and are freely available at cryoem-tools.cloud.
SummaryFull reportAbout validation report
|Date||Deposition: Jun 13, 2018 / Release: Jul 11, 2018|
|Structure viewer||Molecule: |
Downloads & links
Mass: 116602.484 Da / Num. of mol.: 4
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lacZ, b0344, JW0335 / Production host: Escherichia coli (E. coli) / References: UniProt: P00722, beta-galactosidase
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: beta-galactosidase / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Value: 466 kDa/nm / Experimental value: NO|
|Source (natural)||Organism: Escherichia coli (E. coli)|
|Source (recombinant)||Organism: Escherichia coli (E. coli)|
|Buffer solution||pH: 8|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 45 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: D2|
|3D reconstruction||Resolution: 2.2 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 106237 / Symmetry type: POINT|
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