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Yorodumi- PDB-7mh6: Structure of EmrE-D3 mutant in complex with monobody L10 in low p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mh6 | ||||||
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Title | Structure of EmrE-D3 mutant in complex with monobody L10 in low pH (protonated state) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/IMMUNE SYSTEM / small multidrug resistance transporter / TRANSPORT PROTEIN-IMMUNE SYSTEM complex / EmrE / proton bound | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 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 | 7mh6.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mh6.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 7mh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mh6_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 7mh6_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 7mh6_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 7mh6_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/7mh6 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/7mh6 | HTTPS FTP |
-Related structure data
Related structure data | 7mgxC 7ssuC 7sv9C 7svxC 7sztC 7t00C 6wk8S C: citing same article (ref.) S: Starting model for refinement |
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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: Antibody | Mass: 9832.803 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) #2: 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 #3: Water | ChemComp-HOH / | |
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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: 4.37 Å3/Da / Density % sol: 71.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 mM sodium chloride, 100 mM sodium cacodylate, pH 5.5, 34% 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: 0.987 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→70.17 Å / Num. obs: 11183 / % possible obs: 87 % / Redundancy: 6.4 % / CC1/2: 0.994 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.85→3.16 Å / Redundancy: 7.1 % / Num. unique obs: 560 / CC1/2: 0.366 / % possible all: 62.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6WK8 Resolution: 2.85→35.08 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 43.59 / 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: 155.23 Å2 / Biso mean: 94.98 Å2 / Biso min: 43.33 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→35.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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