+Open data
-Basic information
Entry | Database: PDB / ID: 7rr6 | |||||||||
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Title | Multidrug efflux pump subunit AcrB | |||||||||
Components | Multidrug efflux pump subunit AcrB | |||||||||
Keywords | TRANSPORT PROTEIN / Multidrug efflux pump subunit AcrB / NCMN | |||||||||
Function / homology | Function and homology information alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport ...alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Trinh, T.K.H. / Cabezas, A. / Catalano, C. / Qiu, W. / des Georges, A. / Guo, Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Multidrug efflux pump subunit AcrB Authors: Trinh, T.K.H. / Cabezas, A. / Catalano, C. / Qiu, W. / des Georges, A. / Guo, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rr6.cif.gz | 529.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rr6.ent.gz | 429.9 KB | Display | PDB format |
PDBx/mmJSON format | 7rr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rr6_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7rr6_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7rr6_validation.xml.gz | 99.6 KB | Display | |
Data in CIF | 7rr6_validation.cif.gz | 145.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/7rr6 ftp://data.pdbj.org/pub/pdb/validation_reports/rr/7rr6 | HTTPS FTP |
-Related structure data
Related structure data | 24653MC 7rr7C 7rr8C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 114736.289 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: acrB, acrE, b0462, JW0451 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P31224 #2: Chemical | ChemComp-PTY / #3: Chemical | ChemComp-D12 / Has ligand of interest | Y | |
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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: Multidrug efflux pump subunit AcrB / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES |
EM staining | Type: NEGATIVE / Material: 2% uranyl acetate |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 75.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73352 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 6BAJ Accession code: 6BAJ / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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