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- PDB-6drv: Beta-galactosidase -

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Basic information

Entry
Database: PDB / ID: 6drv
TitleBeta-galactosidase
ComponentsBeta-galactosidase
KeywordsHYDROLASE / cryo-EM / Amazon Web Services / RELION
Function / homologyImmunoglobulin-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 sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.2 Å resolution
AuthorsCianfrocco, M.A. / Lahiri, I. / DiMaio, F. / Leschziner, A.E.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 13, 2018 / Release: Jul 11, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 11, 2018Structure modelrepositoryInitial release
1.1Aug 22, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase


Theoretical massNumber of molelcules
Total (without water)466,4104
Polyers466,4104
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Beta-galactosidase / / Beta-gal / Lactase


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: beta-galactosidase / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 466 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2
3D reconstructionResolution: 2.2 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 106237 / Symmetry type: POINT

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