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Yorodumi- PDB-8vxu: Crystal structure of Gdx-Clo A60T from Small Multidrug Resistance... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vxu | ||||||
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Title | Crystal structure of Gdx-Clo A60T from Small Multidrug Resistance family of transporters in complex with cetyltrimetylammonium | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Small Multidrug Resistance / SMR / quaternary ammonium | ||||||
Function / homology | Small drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein / transmembrane transporter activity / plasma membrane / CETYL-TRIMETHYL-AMMONIUM / Multidrug resistance protein, SMR family Function and homology information | ||||||
Biological species | Clostridia bacterium (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Burata, O.E. / Stockbridge, R.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Peripheral positions encode transport specificity in the small multidrug resistance exporters. Authors: Burata, O.E. / O'Donnell, E. / Hyun, J. / Lucero, R.M. / Thomas, J.E. / Gibbs, E.M. / Reacher, I. / Carney, N.A. / 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 | 8vxu.cif.gz | 157 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vxu.ent.gz | 124.4 KB | Display | PDB format |
PDBx/mmJSON format | 8vxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/8vxu ftp://data.pdbj.org/pub/pdb/validation_reports/vx/8vxu | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11787.357 Da / Num. of mol.: 4 / Mutation: A60T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridia bacterium (bacteria) / Gene: sugE / Plasmid: pET21b/sugE_Clo Details (production host): IPTG-induced, Ampicillin Resistance Cell line (production host): Keio / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): E. coli C41(DE3) / Variant (production host): C41 / References: UniProt: U2EQ00 #2: Antibody | Mass: 9832.803 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21b/L10_Mb Details (production host): T7, Kanamycin resistant, IPTG inducible Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-16A / 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: 4.42 Å3/Da / Density meas: 0.335 Mg/m3 / Density % sol: 72.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.75 Details: 100 mM CaCl2, 100 mM N-(2-acetamido)iminodiacetic acid (ADA) pH 6.75, and 33% PEG 600 |
-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: 1.1272 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→70.5 Å / Num. obs: 22068 / % possible obs: 82.1 % / Redundancy: 3.8 % / CC1/2: 0.98 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.29→2.75 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1160 / CC1/2: 0.614 / % possible all: 68.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→35.22 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / Phase error: 37.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→35.22 Å
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Refine LS restraints |
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LS refinement shell |
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