+Open data
-Basic information
Entry | Database: PDB / ID: 6drv | |||||||||
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Title | Beta-galactosidase | |||||||||
Components | Beta-galactosidase | |||||||||
Keywords | HYDROLASE / cryo-EM / Amazon Web Services / RELION | |||||||||
Function / homology | Function and homology information alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Cianfrocco, M.A. / Lahiri, I. / DiMaio, F. / Leschziner, A.E. | |||||||||
Funding support | United States, 2items
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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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6drv.cif.gz | 790.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6drv.ent.gz | 662.3 KB | Display | PDB format |
PDBx/mmJSON format | 6drv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6drv_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6drv_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6drv_validation.xml.gz | 112 KB | Display | |
Data in CIF | 6drv_validation.cif.gz | 173.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/6drv ftp://data.pdbj.org/pub/pdb/validation_reports/dr/6drv | HTTPS FTP |
-Related structure data
Related structure data | 8908MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 116602.484 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: beta-galactosidase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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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
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: D2 (2x2 fold dihedral) |
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106237 / Symmetry type: POINT |