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Yorodumi- PDB-7svx: Structure of EmrE-D3 mutant in complex with monobody L10 and harmane -
+Open data
-Basic information
Entry | Database: PDB / ID: 7svx | ||||||
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Title | Structure of EmrE-D3 mutant in complex with monobody L10 and harmane | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Small Multidrug Resistance transporters / drug efflux pump / EmrE / Membrane protein | ||||||
Function / homology | Function and homology information EmrE multidrug transporter complex / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / xenobiotic transport / response to osmotic stress / xenobiotic transmembrane transporter activity ...EmrE multidrug transporter complex / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / xenobiotic transport / 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 | Escherichia coli (E. coli) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | ||||||
Authors | Kermani, A.A. / Stockbridge, R.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7svx.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7svx.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 7svx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7svx_validation.pdf.gz | 680.3 KB | Display | wwPDB validaton report |
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Full document | 7svx_full_validation.pdf.gz | 689.6 KB | Display | |
Data in XML | 7svx_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 7svx_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/7svx ftp://data.pdbj.org/pub/pdb/validation_reports/sv/7svx | HTTPS FTP |
-Related structure data
Related structure data | 7mgxC 7mh6C 7ssuC 7sv9C 7sztC 7t00C 6wk8S S: Starting model for refinement 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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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.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: emrE, eb, mvrC, b0543, JW0531 / Production host: Escherichia coli (E. coli) / References: UniProt: P23895 #2: Antibody | Mass: 9931.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-CN9 / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9183 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |