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- PDB-7svx: Structure of EmrE-D3 mutant in complex with monobody L10 and harmane -
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Open data
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Basic information
Entry | Database: PDB / ID: 7svx | ||||||
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Title | Structure of EmrE-D3 mutant in complex with monobody L10 and harmane | ||||||
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![]() | TRANSPORT PROTEIN / Small Multidrug Resistance transporters / drug efflux pump / EmrE / Membrane protein | ||||||
Function / homology | ![]() EmrE multidrug transporter complex / choline transmembrane transporter activity / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity ...EmrE multidrug transporter complex / choline transmembrane transporter activity / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity / transmembrane transporter activity / xenobiotic metabolic process / transmembrane transport / cellular response to xenobiotic stimulus / response to xenobiotic stimulus / DNA damage response / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kermani, A.A. / Stockbridge, R.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates. Authors: Kermani, A.A. / Burata, O.E. / Koff, B.B. / Koide, A. / Koide, S. / Stockbridge, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.1 KB | Display | ![]() |
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PDB format | ![]() | 63.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 680.3 KB | Display | ![]() |
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Full document | ![]() | 689.6 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mgxC ![]() 7mh6C ![]() 7ssuC ![]() 7sv9C ![]() 7sztC ![]() 7t00C ![]() 6wk8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11907.279 Da / Num. of mol.: 2 / Mutation: E25N, W31I, V34M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: emrE, eb, mvrC, b0543, JW0531 / Production host: ![]() ![]() #2: Antibody | Mass: 9931.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-CN9 / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.96 Å3/Da / Density % sol: 75.22 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.1 M ammonium sulfate, 0.1 M HEPES, pH 7.1, 33.8% PEG600 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9183 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→114.83 Å / Num. obs: 3378 / % possible obs: 82.1 % / Redundancy: 6.6 % / CC1/2: 0.991 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.921→4.65 Å / Redundancy: 6.7 % / Num. unique obs: 338 / CC1/2: 0.921 / % possible all: 69.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6WK8 Resolution: 3.9→60.21 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 44.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 168.89 Å2 / Biso mean: 62.0083 Å2 / Biso min: 10.9 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.9→60.21 Å
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LS refinement shell | Resolution: 3.9→4.041 Å / Num. reflection Rfree: 135 / Num. reflection Rwork: 24 / Rfactor Rfree error: 0 |